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Gene editing & nucleic-acid machines (PDB): 89 3D models

DNA, RNA, nucleic-acid drugs, gene editing, proteins and 300+ real PDB structures (real sizes 1–100 nm). Each one is a ready-made 3D model you can turn, recolour and place in a figure — open BioDioRama and type its name in the Library search.

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Cas9 with guide RNA and target DNA — Crystal structure of streptococcus pyogenes cas9 in complex with guide rna and target dna — X-ray structure, 2014 (PDB 4OO8), downloaded from the RCSB Protein Data Bank.
Cas9 (apo) — Crystal structure of s. pyogenes cas9 — X-ray structure, 2014 (PDB 4CMP), downloaded from the RCSB Protein Data Bank.
Cas9 R-loop complex — Crystal structure of catalytically-active streptococcus pyogenes crispr-cas9 in complex with single-guided rna and double-stranded dna pr… — X-ray structure, 2016 (PDB 5F9R), downloaded from the RCSB Protein Data Bank.
Cas12a (Cpf1) with crRNA and DNA — Crystal structure of acidaminococcus sp. cpf1 in complex with crrna and target dna — X-ray structure, 2016 (PDB 5B43), downloaded from the RCSB Protein Data Bank.
Cas13a (C2c2) with crRNA — Crystal structure of lbacas13a (c2c2) bound to mature crrna (24-nt spacer) — X-ray structure, 2017 (PDB 5W1H), downloaded from the RCSB Protein Data Bank.
Adenine base editor ABE8e — Structure of the spcas9 dna adenine base editor - abe8e — cryo-EM structure, 2020 (PDB 6VPC), downloaded from the RCSB Protein Data Bank.
TAL effector bound to DNA — Structure of tal effector pthxo1 bound to its dna target — X-ray structure, 2012 (PDB 3UGM), downloaded from the RCSB Protein Data Bank.
Zif268 zinc fingers bound to DNA — Zif268 zinc finger-dna complex — X-ray structure, 1997 (PDB 1AAY), downloaded from the RCSB Protein Data Bank.
Human Argonaute-2 with microRNA — Crystal structure of human argonaute2 — X-ray structure, 2014 (PDB 4OLA), downloaded from the RCSB Protein Data Bank.
Argonaute-2 with guide RNA — The crystal structure of human argonaute2 bound to a defined guide rna — X-ray structure, 2014 (PDB 4W5N), downloaded from the RCSB Protein Data Bank.
Human Dicer with pre-miRNA — Cryo-em structure of human dicer and its complexes with a pre-mirna substrate — cryo-EM structure, 2018 (PDB 5ZAL), downloaded from the RCSB Protein Data Bank.
Argonaute (Aquifex) with siRNA — Crystal structure of aa-ago with externally-bound sirna — X-ray structure, 2006 (PDB 2F8S), downloaded from the RCSB Protein Data Bank.
RNA polymerase II — Rna polymerase ii crystal form ii at 2.8 a resolution — X-ray structure, 2001 (PDB 1I50), downloaded from the RCSB Protein Data Bank.
T7 RNA polymerase — Structural basis for the transition from initiation to elongation transcription in t7 rna polymerase — X-ray structure, 2002 (PDB 1MSW), downloaded from the RCSB Protein Data Bank.
DNA polymerase I (Klenow) — Dna polymerase i klenow fragment (e.c.2.7.7.7) mutant/dna complex — X-ray structure, 1994 (PDB 1KLN), downloaded from the RCSB Protein Data Bank.
Taq DNA polymerase — Structure of taq dna polymerase — X-ray structure, 1996 (PDB 1TAQ), downloaded from the RCSB Protein Data Bank.
EcoRI bound to DNA — X-ray structure of the dna-eco ri endonuclease-dna recognition complex: the recognition network and the integration of recognition and cl… — X-ray structure, 1995 (PDB 1ERI), downloaded from the RCSB Protein Data Bank.
EcoRV bound to DNA — Mg2+ binding to the active site of eco rv endonuclease: a crystallographic study of complexes with substrate and product dna at 2 angstro… — X-ray structure, 1995 (PDB 1RVA), downloaded from the RCSB Protein Data Bank.
BamHI bound to DNA — Restriction endonuclease bamhi complex with dna — X-ray structure, 1995 (PDB 1BHM), downloaded from the RCSB Protein Data Bank.
Topoisomerase I bound to DNA — Topoisomerase i/dna complex — X-ray structure, 1998 (PDB 1A36), downloaded from the RCSB Protein Data Bank.
eIF4E bound to mRNA cap — Cocrystal structure of the messenger rna 5' cap-binding protein (eif4e) bound to 7-methyl-gdp — X-ray structure, 2000 (PDB 1EJ1), downloaded from the RCSB Protein Data Bank.
Poly(A)-binding protein with RNA — X-ray crystal structure of the poly(a)-binding protein in complex with polyadenylate rna — X-ray structure, 1999 (PDB 1CVJ), downloaded from the RCSB Protein Data Bank.
E. coli 70S ribosome — High-resolution structure of the escherichia coli ribosome — X-ray structure, 2015 (PDB 4YBB), downloaded from the RCSB Protein Data Bank.
50S ribosomal subunit — Crystal structure of the large ribosomal subunit from haloarcula marismortui at 2.4 angstrom resolution — X-ray structure, 2000 (PDB 1FFK), downloaded from the RCSB Protein Data Bank.
30S ribosomal subunit — Structure of the thermus thermophilus 30s ribosomal subunit — X-ray structure, 2002 (PDB 1J5E), downloaded from the RCSB Protein Data Bank.
Transfer RNA (tRNA-Phe) — The crystal structure of yeast phenylalanine trna at 1.93 a resolution — X-ray structure, 2000 (PDB 1EHZ), downloaded from the RCSB Protein Data Bank.
Hammerhead ribozyme — Three-dimensional structure of a hammerhead ribozyme — X-ray structure, 1995 (PDB 1HMH), downloaded from the RCSB Protein Data Bank.
Group I intron P4-P6 domain — Crystal structure of a group i ribozyme domain: principles of rna packing — X-ray structure, 1996 (PDB 1GID), downloaded from the RCSB Protein Data Bank.
Purine riboswitch — A-riboswitch-adenine complex — X-ray structure, 2004 (PDB 1Y26), downloaded from the RCSB Protein Data Bank.
TPP riboswitch — Crystal structure of thiamine pyrophosphate-specific riboswitch in complex with thiamine pyrophosphate — X-ray structure, 2006 (PDB 2GDI), downloaded from the RCSB Protein Data Bank.
Nucleosome core particle — X-ray structure of the nucleosome core particle, ncp147, at 1.9 a resolution — X-ray structure, 2002 (PDB 1KX5), downloaded from the RCSB Protein Data Bank.
Nucleosome (histones + DNA) — Complex between nucleosome core particle (h3,h4,h2a,h2b) and 146 bp long dna fragment — X-ray structure, 1998 (PDB 1AOI), downloaded from the RCSB Protein Data Bank.
B-DNA dodecamer — Structure of a b-dna dodecamer. conformation and dynamics — X-ray structure, 1981 (PDB 1BNA), downloaded from the RCSB Protein Data Bank.
B-DNA 16-mer — Crystal structure analysis of a 16-base-pair b-dna — X-ray structure, 2008 (PDB 3BSE), downloaded from the RCSB Protein Data Bank.
Z-DNA — Molecular structure of a left-handed double helical dna fragment at atomic resolution — X-ray structure, 1989 (PDB 2DCG), downloaded from the RCSB Protein Data Bank.
Human telomeric G-quadruplex — Structure and packing of human telomeric dna — X-ray structure, 2002 (PDB 1KF1), downloaded from the RCSB Protein Data Bank.
G-quadruplex DNA — Solution structure of the human telomeric repeat d(ag3[t2ag3]3) of the g-quadruplex — NMR structure, 1994 (PDB 143D), downloaded from the RCSB Protein Data Bank.
Thrombin-binding DNA aptamer — Three-dimensional solution structure of the thrombin binding dna aptamer d(ggttggtgtggttgg) — NMR structure, 1994 (PDB 148D), downloaded from the RCSB Protein Data Bank.
Thrombin bound to DNA aptamer — X-ray structure of the complex between human alpha thrombin and thrombin binding aptamer in the presence of sodium ions — X-ray structure, 2012 (PDB 4DIH), downloaded from the RCSB Protein Data Bank.
Spinach RNA aptamer — Crystal structure of an rna aptamer in complex with fluorophore and fab — X-ray structure, 2014 (PDB 4KZD), downloaded from the RCSB Protein Data Bank.
MS2 coat protein bound to RNA — Rna bacteriophage ms2 coat protein/rna complex — X-ray structure, 1997 (PDB 1ZDI), downloaded from the RCSB Protein Data Bank.
RNA duplex — Crystallographic structure of an rna helix: [u(u-a)6a]2 — X-ray structure, 1991 (PDB 1RNA), downloaded from the RCSB Protein Data Bank.
AP2 clathrin adaptor core — Ap2 clathrin adaptor core — X-ray structure, 2007 (PDB 2VGL), downloaded from the RCSB Protein Data Bank.
Cas9 (HiFi) complex — Conformational states of cas9-sgrna-dna ternary complex in the presence of magnesium — cryo-EM structure, 2019 (PDB 6O0Z), downloaded from the RCSB Protein Data Bank.
Cas9–sgRNA–DNA (SaCas9) — Cryo-em structure of spcas9-sgrna-dna ternary complex — cryo-EM structure, 2017 (PDB 5Y36), downloaded from the RCSB Protein Data Bank.
SaCas9 with sgRNA and DNA — Crystal structure of staphylococcus aureus cas9 in complex with sgrna and target dna (ttgggt pam) — X-ray structure, 2015 (PDB 5AXW), downloaded from the RCSB Protein Data Bank.
Cas13a with crRNA — Crystal structure of lbucas13a-crrna-target rna ternary complex — X-ray structure, 2017 (PDB 5XWP), downloaded from the RCSB Protein Data Bank.
Cas13b — High-resolution crystal structure of cas13b from prevotella buccae — X-ray structure, 2019 (PDB 6DTD), downloaded from the RCSB Protein Data Bank.
Cascade with crRNA — Crystal structure of a crispr rna-guided surveillance complex, cascade, bound to a ssdna target — X-ray structure, 2014 (PDB 4QYZ), downloaded from the RCSB Protein Data Bank.
Cas9 inhibited by anti-CRISPR AcrIIA2 — Crystal structure of acriia2-spycas9-sgrna ternary complex — X-ray structure, 2019 (PDB 6IFO), downloaded from the RCSB Protein Data Bank.
Topoisomerase — Crystal structure of heterodimeric l. donovani topoisomerase i-vanadate-dna complex — X-ray structure, 2006 (PDB 2B9S), downloaded from the RCSB Protein Data Bank.
Tetranucleosome (chromatin fibre) — Structure of the 4_601_167 tetranucleosome — X-ray structure, 2005 (PDB 1ZBB), downloaded from the RCSB Protein Data Bank.
DNA ligase I — Crystal structure of human dna ligase i bound to 5'-adenylated, nicked dna — X-ray structure, 2004 (PDB 1X9N), downloaded from the RCSB Protein Data Bank.
Pol β with DNA — Thermostable b type dna polymerase from thermococcus gorgonarius — X-ray structure, 1999 (PDB 1TGO), downloaded from the RCSB Protein Data Bank.
Taq polymerase ternary complex — Crystal structure of an active ternary complex of the large fragment of dna polymerase i from thermus aquaticus — X-ray structure, 1999 (PDB 3KTQ), downloaded from the RCSB Protein Data Bank.
T7 DNA polymerase — T7 dna polymerase complexed to dna primer/template,a nucleoside triphosphate, and its processivity factor thioredoxin — X-ray structure, 1998 (PDB 1T7P), downloaded from the RCSB Protein Data Bank.
Taq with DNA — Ddgtp-trapped closed ternary complex of the large fragment of dna polymerase i from thermus aquaticus — X-ray structure, 1999 (PDB 1QSS), downloaded from the RCSB Protein Data Bank.
Reverse transcriptase with DNA — Crystal structure of a. fulgidus fen-1 bound to dna — X-ray structure, 2004 (PDB 1RXW), downloaded from the RCSB Protein Data Bank.
RNA polymerase I — Structure of the rna polymerase lambda-based antitermination complex — cryo-EM structure, 2019 (PDB 6GOV), downloaded from the RCSB Protein Data Bank.
Spliceosome — Post-catalytic p complex spliceosome with 3' splice site docked — cryo-EM structure, 2018 (PDB 6EXN), downloaded from the RCSB Protein Data Bank.
Human U4/U6.U5 tri-snRNP (spliceosome) — 3d structure determination of the human*u4/u6.u5* tri-snrnp complex — cryo-EM structure, 2016 (PDB 3JCR), downloaded from the RCSB Protein Data Bank.
Ribosome (70S) with tRNAs — Structures of the bacterial ribosome in classical and hybrid states of trna binding — X-ray structure, 2014 (PDB 4V9D), downloaded from the RCSB Protein Data Bank.
Human 80S ribosome — Structure of the human 80s ribosome — cryo-EM structure, 2015 (PDB 4UG0), downloaded from the RCSB Protein Data Bank.
Human 80S ribosome — Structure of the human 80s ribosome — cryo-EM structure, 2014 (PDB 4V6X), downloaded from the RCSB Protein Data Bank.
70S ribosome with mRNA — Crystal structure of the thermus thermophilus 70s ribosome in the pre-attack state of peptide bond formation containing acylated trna-sub… — X-ray structure, 2014 (PDB 1VY4), downloaded from the RCSB Protein Data Bank.
Ribosome with antibiotic — Structure of the 80s mammalian ribosome bound to eef2 — cryo-EM structure, 2014 (PDB 3J7P), downloaded from the RCSB Protein Data Bank.
30S with antibiotics — Structure of the thermus thermophilus 30s ribosomal subunit in complex with the antibiotics streptomycin, spectinomycin, and paromomycin — X-ray structure, 2000 (PDB 1FJG), downloaded from the RCSB Protein Data Bank.
Ribosome with tRNA — Crystal structure of the bacterial ribosome from escherichia coli at 3.5 a resolution. — X-ray structure, 2014 (PDB 4V4Q), downloaded from the RCSB Protein Data Bank.
tRNA synthetase with tRNA — Crystal structure of thermus thermophilus valyl-trna synthetase complexed with trna(val) and valyl-adenylate analogue — X-ray structure, 2000 (PDB 1GAX), downloaded from the RCSB Protein Data Bank.
EF-Tu with tRNA — Structure of e. coli threonyl-trna synthetase complexed with its cognate trna — X-ray structure, 1999 (PDB 1QF6), downloaded from the RCSB Protein Data Bank.
EF-Tu–tRNA ternary — Phe-trna, elongation factor ef-tu:gdpnp ternary complex — X-ray structure, 1996 (PDB 1TTT), downloaded from the RCSB Protein Data Bank.
Signal recognition particle on the ribosome — Model of e. coli srp bound to 70s rncs — cryo-EM structure, 2006 (PDB 2J28), downloaded from the RCSB Protein Data Bank.
Full-length hammerhead ribozyme — High-resolution full-length hammerhead ribozyme — X-ray structure, 2013 (PDB 3ZP8), downloaded from the RCSB Protein Data Bank.
Riboswitch — Structure of the thf riboswitch — X-ray structure, 2014 (PDB 4LVV), downloaded from the RCSB Protein Data Bank.
RNase P RNA (specificity domain) — Crystal structure of the specificity domain of ribonuclease p of the a-type — X-ray structure, 2004 (PDB 1U9S), downloaded from the RCSB Protein Data Bank.
M-box riboswitch — Structure of the m-box riboswitch aptamer domain — X-ray structure, 2007 (PDB 2QBZ), downloaded from the RCSB Protein Data Bank.
50S subunit with puromycin analogue — Large ribosomal subunit complexed with r(cc)-da-puromycin — X-ray structure, 2000 (PDB 1FFZ), downloaded from the RCSB Protein Data Bank.
Yeast RNase P — Cryo-em structure of yeast ribonuclease p — cryo-EM structure, 2018 (PDB 6AGB), downloaded from the RCSB Protein Data Bank.
ZMP riboswitch — The structure of a pfi riboswitch bound to zmp — X-ray structure, 2015 (PDB 4ZNP), downloaded from the RCSB Protein Data Bank.
RNA aptamer with neomycin — Saccharide-rna recognition in the neomycin b / rna aptamer complex — NMR structure, 1999 (PDB 1NEM), downloaded from the RCSB Protein Data Bank.
ATP aptamer — Amp rna aptamer complex, nmr, 8 structures — NMR structure, 1997 (PDB 1AM0), downloaded from the RCSB Protein Data Bank.
MUC1 DNA aptamer — Solution structure of truncated 23-mer dna muc1 aptamer — NMR structure, 2011 (PDB 2L5K), downloaded from the RCSB Protein Data Bank.
G-quadruplex — G-quadruplex structure formed at the 5'-end of nheiii_1 element in human c-myc promoter — NMR structure, 2012 (PDB 2LBY), downloaded from the RCSB Protein Data Bank.
DNA with Gal4 — Dna recognition by gal4: structure of a protein/dna complex — X-ray structure, 1992 (PDB 1D66), downloaded from the RCSB Protein Data Bank.
GCN4 bZIP with DNA — The gcn4 basic region leucine zipper binds dna as a dimer of uninterrupted alpha helices: crystal structure of the protein-dna complex — X-ray structure, 1993 (PDB 1YSA), downloaded from the RCSB Protein Data Bank.
p53 with DNA — Tumor suppressor p53 complexed with dna — X-ray structure, 1995 (PDB 1TUP), downloaded from the RCSB Protein Data Bank.
HIV nucleocapsid with RNA — Structure of the hiv-1 nucleocapsid protein bound to the sl3 psi-rna recognition element, nmr, 25 structures — NMR structure, 1998 (PDB 1A1T), downloaded from the RCSB Protein Data Bank.
Argonaute-2 with miRNA and target — Human argonaute2 bound to t1-g target rna — X-ray structure, 2015 (PDB 4Z4D), downloaded from the RCSB Protein Data Bank.
Argonaute-2 with guide RNA — The crystal structure of human argonaute2 bound to a guide and target rna containing seed pairing from 2-9 — X-ray structure, 2014 (PDB 4W5O), downloaded from the RCSB Protein Data Bank.