6VPC: SpCas9 DNA adenine base editor - ABE8e

Structure of the SpCas9 DNA adenine base editor - ABE8e. Determined by electron microscopy at 3.2 Å resolution. Released 29 Jul 2020.

Method: Electron microscopy
Resolution: 3.2 Å
Organisms: Streptococcus pyogenes, synthetic construct, Escherichia coli
Chains: 6
Atoms: 16,309
Mol. weight: 264.58 kDa
Ligands: ZN, MG
Released: 29 Jul 2020

Explore 6VPC in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6VPC contains 96 α-helices and 68 β-strands across 3 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain B: 84 helices, 52 β-strands

Element	Residues	Length	Sheet
β-strand	202-208	7	1
β-strand	212-219	8	1
α-helix	223-225	3
β-strand	226-230	5	2
β-strand	231-233	3	3
β-strand	239-243	5	2
β-strand	245-249	5	1
α-helix	251-253	3
α-helix	257-290	34
α-helix	294-299	6
α-helix	319-328	10
α-helix	332-341	10
α-helix	348-360	13
β-strand	364	1	4
α-helix	379-392	14
α-helix	397-399	3
α-helix	405-410	6
α-helix	415-424	10
α-helix	434-442	9
β-strand	448	1	5
β-strand	460	1	5
α-helix	468-479	12
α-helix	481-483	3
α-helix	484-498	15
α-helix	500-503	4
α-helix	513-539	27
α-helix	541-543	3
α-helix	544-548	5
α-helix	556-560	5
α-helix	566-579	14
α-helix	584-591	8
α-helix	604-606	3
β-strand	608	1	4
α-helix	609-623	15
α-helix	628-632	5
α-helix	634-642	9
β-strand	664	1	6
α-helix	669-670	2
α-helix	675-678	4
β-strand	679	1	6
α-helix	681-690	10
α-helix	694	1
β-strand	695	1	7
α-helix	696	1
β-strand	703	1	7
β-strand	704-706	3	8
α-helix	710-721	12
β-strand	725-726	2	9
β-strand	735-736	2	9
α-helix	739-745	7
α-helix	746-750	5
β-strand	757	1	10
α-helix	758-760	3
α-helix	761-767	7
α-helix	768-770	3
β-strand	783	1	10
α-helix	789-798	10
α-helix	801-805	5
α-helix	807-809	3
α-helix	810-822	13
α-helix	826-833	8
α-helix	834-838	5
α-helix	842-850	9
β-strand	856-860	5	8
α-helix	861-865	5
α-helix	876-881	6
α-helix	890-895	6
α-helix	901-905	5
α-helix	917-922	6
α-helix	928-947	20
α-helix	951-953	3
β-strand	955-960	6	1
α-helix	974-988	15
α-helix	992-995	4
α-helix	1000-1002	3
α-helix	1006-1013	8
β-strand	1017	1	11
β-strand	1024	1	11
α-helix	1030-1032	3
β-strand	1034-1037	4	12
α-helix	1049-1051	3
β-strand	1052-1055	4	12
α-helix	1058-1061	4
α-helix	1070-1085	16
α-helix	1091-1101	11
α-helix	1123-1136	14
β-strand	1140	1	13
β-strand	1146	1	13
β-strand	1151-1155	5	1
α-helix	1157-1167	11
α-helix	1178-1197	20
α-helix	1199-1201	3
α-helix	1202-1205	4
β-strand	1206	1	1
α-helix	1217-1219	3
α-helix	1228-1239	12
α-helix	1240-1243	4
β-strand	1246-1249	4	14
β-strand	1253-1256	4	14
β-strand	1260-1262	3	15
β-strand	1269-1272	4	15
α-helix	1276-1284	9
β-strand	1290-1293	4	1
β-strand	1303	1	16
β-strand	1308	1	17
α-helix	1309-1310	2
β-strand	1317-1318	2	17
α-helix	1325-1328	4
β-strand	1330-1331	2	17
β-strand	1334	1	16
α-helix	1335	1
β-strand	1336-1348	13	18
β-strand	1353-1364	12	18
α-helix	1368-1373	6
α-helix	1375-1382	8
β-strand	1385	1	18
α-helix	1389-1391	3
β-strand	1393-1395	3	18
β-strand	1400-1402	3	3
α-helix	1404-1406	3
β-strand	1408-1411	4	3
β-strand	1417-1419	3	3
α-helix	1427-1437	11
α-helix	1446-1458	13
α-helix	1461-1473	13
α-helix	1474-1478	5
α-helix	1481-1493	13
α-helix	1499-1508	10
α-helix	1509-1512	4
β-strand	1516	1	3
β-strand	1521-1523	3	19
β-strand	1526-1528	3	19
β-strand	1533	1	3
α-helix	1538-1541	4
β-strand	1543-1547	5	3
β-strand	1554-1558	5	3

Chain E: 5 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	8-24	17
β-strand	31-36	6	20
β-strand	39-45	7	20
α-helix	48-51	4
α-helix	58-70	13
β-strand	79-82	4	20
β-strand	84	1	21
α-helix	88-97	10
β-strand	101-103	3	20
β-strand	106	1	21
β-strand	114	1	22
β-strand	119	1	22
β-strand	131-133	3	20
α-helix	138-148	11

Chain F: 7 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	8-24	17
β-strand	31-36	6	23
β-strand	39-45	7	23
α-helix	48-51	4
α-helix	58-70	13
β-strand	79-82	4	23
α-helix	88-97	10
β-strand	101-104	4	23
β-strand	114	1	24
β-strand	119	1	24
α-helix	129-130	2
β-strand	131-133	3	23
α-helix	138-149	12
α-helix	154-159	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Cas9 (SpCas9) single-guide RNA (sgRNA)	A	RNA	82	Streptococcus pyogenes
CRISPR-associated endonuclease Cas9	B	protein	1361	Streptococcus pyogenes	Q99ZW2 (AlphaFold model)
DNA target strand (TS)	C	DNA	50	synthetic construct
DNA non-target strand (NTS)	D	DNA	50	synthetic construct
t-RNA adenine deaminase A v8e (TadA-8e)	E, F	protein	227	Escherichia coli	P68398 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6VPC_1 Cas9 (SpCas9) single-guide RNA (sgRNA) (chains A)
GGUUCCACUUUCUUAGACUGAGUUUUAGAGCUAGAAAUAGCAAGUUAAAAUAAGGCUAGU
CCGUUAUCAACUUGAAAAAGUG

Sequence of entity 2 (B), FASTA

>6VPC_2 CRISPR-associated endonuclease Cas9 (chains B)
KYSIGLAIGTNSVGWAVITDEYKVPSKKFKVLGNTDRHSIKKNLIGALLFDSGETAEATR
LKRTARRRYTRRKNRICYLQEIFSNEMAKVDDSFFHRLEESFLVEEDKKHERHPIFGNIV
DEVAYHEKYPTIYHLRKKLVDSTDKADLRLIYLALAHMIKFRGHFLIEGDLNPDNSDVDK
LFIQLVQTYNQLFEENPINASGVDAKAILSARLSKSRRLENLIAQLPGEKKNGLFGNLIA
LSLGLTPNFKSNFDLAEDAKLQLSKDTYDDDLDNLLAQIGDQYADLFLAAKNLSDAILLS
DILRVNTEITKAPLSASMIKRYDEHHQDLTLLKALVRQQLPEKYKEIFFDQSKNGYAGYI
DGGASQEEFYKFIKPILEKMDGTEELLVKLNREDLLRKQRTFDNGSIPHQIHLGELHAIL
RRQEDFYPFLKDNREKIEKILTFRIPYYVGPLARGNSRFAWMTRKSEETITPWNFEEVVD
KGASAQSFIERMTNFDKNLPNEKVLPKHSLLYEYFTVYNELTKVKYVTEGMRKPAFLSGE
QKKAIVDLLFKTNRKVTVKQLKEDYFKKIECFDSVEISGVEDRFNASLGTYHDLLKIIKD
KDFLDNEENEDILEDIVLTLTLFEDREMIEERLKTYAHLFDDKVMKQLKRRRYTGWGRLS
RKLINGIRDKQSGKTILDFLKSDGFANRNFMQLIHDDSLTFKEDIQKAQVSGQGDSLHEH
IANLAGSPAIKKGILQTVKVVDELVKVMGRHKPENIVIEMARENQTTQKGQKNSRERMKR
IEEGIKELGSQILKEHPVENTQLQNEKLYLYYLQNGRDMYVDQELDINRLSDYDVDAIVP
QSFLKDDSIDNKVLTRSDKNRGKSDNVPSEEVVKKMKNYWRQLLNAKLITQRKFDNLTKA
ERGGLSELDKAGFIKRQLVETRQITKHVAQILDSRMNTKYDENDKLIREVKVITLKSKLV
SDFRKDFQFYKVREINNYHHAHDAYLNAVVGTALIKKYPKLESEFVYGDYKVYDVRKMIA
KSEQEIGKATAKYFFYSNIMNFFKTEITLANGEIRKRPLIETNGETGEIVWDKGRDFATV
RKVLSMPQVNIVKKTEVQTGGFSKESILPKRNSDKLIARKKDWDPKKYGGFDSPTVAYSV
LVVAKVEKGKSKKLKSVKELLGITIMERSSFEKNPIDFLEAKGYKEVKKDLIIKLPKYSL
FELENGRKRMLASAGELQKGNELALPSKYVNFLYLASHYEKLKGSPEDNEQKQLFVEQHK
HYLDEIIEQISEFSKRVILADANLDKVLSAYNKHRDKPIREQAENIIHLFTLTNLGAPAA
FKYFDTTIDRKRYTSTKEVLDATLIHQSITGLYETRIDLSQ

Sequence of entity 3 (C), FASTA

>6VPC_3 DNA target strand (TS) (chains C)
CTAATCGCCCTCAGTCTAAGAAAGTGGAACACGGTCGGAGCCACCGATCG

Sequence of entity 4 (D), FASTA

>6VPC_4 DNA non-target strand (NTS) (chains D)
CGATCGGTGGCTCCGACCGTGTTCCXCTTTCTTAGACTGAGGGCGATTAG

Sequence of entity 5 (E, F), FASTA

>6VPC_5 t-RNA adenine deaminase A v8e (TadA-8e) (chains E, F)
MGSSHHHHHHMKRTADGSEFESPKKKRKVSEVEFSHEYWMRHALTLAKRARDEREVPVGA
VLVLNNRVIGEGWNRAIGLHDPTAHAEIMALRQGGLVMQNYRLIDATLYVTFEPCVMCAG
AMIHSRIGRVVFGVRNSKRGAAGSLMNVLNYPGMNHRVEITEGILADECAALLCDFYRMP
RQVFNAQKKAQSSINSGGSSGGSSGSETPGTSESATPESSGGSSGGS

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2
MG	Magnesium ion	Mg	3

Primary citation

DNA capture by a CRISPR-Cas9-guided adenine base editor. Lapinaite, A., Knott, G.J., Palumbo, C.M. et al. Science (2020) 369:566-571. DOI 10.1126/science.abb1390 · PubMed

Other PDB entries of the same protein (UniProt Q99ZW2 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8SCA 1.67 Å, Rec3 Domain from S. pyogenes Cas9
6O56 1.9 Å, HNH Nuclease from S. pyogenes Cas9
5B2R 2.0 Å, Crystal structure of the Streptococcus pyogenes Cas9 VQR variant in complex with sgRNA…
5FQ5 2.14 Å, Crystal structure of Cas9-sgRNA-DNA complex solved by native SAD phasing
7OXA 2.15 Å, Target-bound SpCas9 complex with AAVS1 chimeric RNA-DNA guide
5B2S 2.2 Å, Crystal structure of the Streptococcus pyogenes Cas9 EQR variant in complex with sgRNA…
5B2T 2.2 Å, Crystal structure of the Streptococcus pyogenes Cas9 VRER variant in complex with sgRNA…
7QQV 2.25 Å, SpCas9 bound to FANCF off-target3 DNA substrate
7QQZ 2.25 Å, SpCas9 bound to FANCF off-target7 DNA substrate
7QR0 2.3 Å, SpCas9 bound to TRAC off-target1 DNA substrate
4UN4 2.37 Å, Crystal structure of Cas9 bound to PAM-containing DNA target with mismatches at…
4UN5 2.4 Å, Crystal structure of Cas9 bound to PAM-containing DNA target containing mismatches at…

Browse more

6VPC is part of these collections:

CRISPR and genome editing

About this viewer

MolViewer shows 6VPC directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.