6WGE: Human Cohesin-NIPBL-DNA complex without STAG1

Cryo-EM structure of human Cohesin-NIPBL-DNA complex without STAG1. Determined by electron microscopy at 3.9 Å resolution. Released 20 May 2020.

Method: Electron microscopy
Resolution: 3.9 Å
Organism: Homo sapiens
Chains: 6
Atoms: 20,194
Mol. weight: 571.11 kDa
Ligands: MG, ANP
Released: 20 May 2020

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

Secondary structure: helices and β-sheets

6WGE contains 105 α-helices and 40 β-strands across 4 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 A: 12 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	3-10	8	1
β-strand	12	1	2
β-strand	18-20	3	1
α-helix	21-24	4
β-strand	27-29	3	3
α-helix	39-48	10
α-helix	53-56	4
β-strand	65	1	2
β-strand	79-86	8	1
β-strand	90-92	3	1
β-strand	94-99	6	1
β-strand	102-107	6	1
β-strand	111-112	2	1
α-helix	114-124	11
β-strand	134	1	3
α-helix	139-144	6
α-helix	148-158	11
α-helix	165-198	34
α-helix	1035-1088	54
β-strand	1096-1100	5	4
α-helix	1106-1108	3
β-strand	1111-1115	5	4
α-helix	1130-1147	18
β-strand	1152-1156	5	3
α-helix	1164-1178	15
β-strand	1183-1187	5	3
α-helix	1191-1194	4
β-strand	1199-1206	8	3
β-strand	1212-1219	8	3

Chain B: 17 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	5
β-strand	16-17	2	5
α-helix	21-23	3
β-strand	28-30	3	6
α-helix	39-49	11
α-helix	51-53	3
α-helix	58-62	5
β-strand	76-82	7	5
β-strand	96-102	7	5
β-strand	107-111	5	5
β-strand	114-115	2	5
α-helix	120-128	9
β-strand	138-139	2	6
α-helix	145-147	3
α-helix	152-163	12
α-helix	167-235	69
α-helix	935-946	12
α-helix	964-978	15
β-strand	984	1	7
α-helix	986-1047	62
β-strand	1052-1057	6	8
β-strand	1096-1101	6	8
α-helix	1117-1134	18
β-strand	1139-1142	4	6
α-helix	1145-1147	3
α-helix	1151-1164	14
β-strand	1169-1173	5	6
α-helix	1177-1181	5
β-strand	1188-1192	5	9
β-strand	1195-1199	5	9
α-helix	1203-1207	5
α-helix	1208-1212	5

Chain C: 8 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	15-22	8
α-helix	29-34	6
α-helix	38-45	8
α-helix	53-85	33
β-strand	89	1	7
β-strand	158	1	10
α-helix	167-170	4
α-helix	559-571	13
β-strand	579-580	2	11
α-helix	581-584	4
α-helix	590-605	16
β-strand	609-612	4	11
β-strand	621-624	4	11

Chain E: 68 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	1199-1215	17
α-helix	1235-1243	9
α-helix	1244-1248	5
α-helix	1249-1252	4
α-helix	1258-1272	15
α-helix	1295-1318	24
α-helix	1330-1343	14
α-helix	1344-1348	5
α-helix	1349-1352	4
α-helix	1381-1403	23
α-helix	1408-1419	12
α-helix	1420-1423	4
α-helix	1428-1444	17
α-helix	1449-1457	9
β-strand	1473	1	12
β-strand	1487	1	12
α-helix	1490-1500	11
α-helix	1525-1550	26
α-helix	1559-1571	13
α-helix	1581-1596	16
α-helix	1604-1627	24
α-helix	1647-1665	19
α-helix	1669-1689	21
α-helix	1709-1727	19
α-helix	1750-1763	14
α-helix	1767-1769	3
α-helix	1770-1780	11
α-helix	1786-1802	17
α-helix	1810-1820	11
β-strand	1822	1	10
α-helix	1825-1841	17
α-helix	1850-1854	5
α-helix	1855-1857	3
α-helix	1863-1878	16
α-helix	1885-1894	10
α-helix	1895-1897	3
α-helix	1901-1913	13
α-helix	1923-1940	18
α-helix	1946-1957	12
α-helix	1966-1985	20
α-helix	1999-2015	17
α-helix	2018-2020	3
α-helix	2024-2032	9
α-helix	2038-2054	17
α-helix	2055-2057	3
α-helix	2063-2077	15
α-helix	2082-2098	17
α-helix	2103-2125	23
α-helix	2133-2153	21
α-helix	2159-2162	4
α-helix	2169-2181	13
α-helix	2187-2202	16
α-helix	2204-2208	5
α-helix	2210-2219	10
α-helix	2228-2252	25
α-helix	2259-2261	3
α-helix	2274-2288	15
α-helix	2296-2309	14
α-helix	2321-2325	5
α-helix	2332-2348	17
α-helix	2352-2355	4
α-helix	2358-2371	14
α-helix	2393-2399	7
α-helix	2403-2417	15
α-helix	2425-2437	13
α-helix	2444-2470	27
α-helix	2534-2557	24
α-helix	2561-2566	6
α-helix	2578-2581	4
α-helix	2589-2600	12
α-helix	2608-2625	18

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Structural maintenance of chromosomes protein 1A	A	protein	1233	Homo sapiens	Q14683 (AlphaFold model)
Structural maintenance of chromosomes protein 3	B	protein	1217	Homo sapiens	Q9UQE7 (AlphaFold model)
Double-strand-break repair protein rad21 homolog	C	protein	631	Homo sapiens	O60216 (AlphaFold model)
Nipped-B-like protein	E	protein	1642	Homo sapiens	Q6KC79 (AlphaFold model)
DNA (43-mer)	F	DNA	43	Homo sapiens
DNA (43-mer)	G	DNA	43	Homo sapiens

Sequence of entity 1 (A), FASTA

>6WGE_1 Structural maintenance of chromosomes protein 1A (chains A)
MGFLKLIEIENFKSYKGRQIIGPFQRFTAIIGPNGSGKSNLMDAISFVLGEKTSNLRVKT
LRDLIHGAPVGKPAANRAFVSMVYSEEGAEDRTFARVIVGGSSEYKINNKVVQLHEYSEE
LEKLGILIKARNFLVFQGAVESIAMKNPKERTALFEEISRSGELAQEYDKRKKEMVKAEE
DTQFNYHRKKNIAAERKEAKQEKEEADRYQRLKDEVVRAQVQLQLFKLYHNEVEIEKLNK
ELASKNKEIEKDKKRMDKVEDELKEKKKELGKMMREQQQIEKEIKEKDSELNQKRPQYIK
AKENTSHKIKKLEAAKKSLQNAQKHYKKRKGDMDELEKEMLSVEKARQEFEERMEEESQS
QGRDLTLEENQVKKYHRLKEEASKRAATLAQELEKFNRDQKADQDRLDLEERKKVETEAK
IKQKLREIEENQKRIEKLEEYITTSKQSLEEQKKLEGELTEEVEMAKRRIDEINKELNQV
MEQLGDARIDRQESSRQQRKAEIMESIKRLYPGSVYGRLIDLCQPTQKKYQIAVTKVLGK
NMDAIIVDSEKTGRDCIQYIKEQRGEPETFLPLDYLEVKPTDEKLRELKGAKLVIDVIRY
EPPHIKKALQYACGNALVCDNVEDARRIAFGGHQRHKTVALDGTLFQKSGVISGGASDLK
AKARRWDEKAVDKLKEKKERLTEELKEQMKAKRKEAELRQVQSQAHGLQMRLKYSQSDLE
QTKTRHLALNLQEKSKLESELANFGPRINDIKRIIQSREREMKDLKEKMNQVEDEVFEEF
CREIGVRNIREFEEEKVKRQNEIAKKRLEFENQKTRLGIQLDFEKNQLKEDQDKVHMWEQ
TVKKDENEIEKLKKEEQRHMKIIDETMAQLQDLKNQHLAKKSEVNDKNHEMEEIRKKLGG
ANKEMTHLQKEVTAIETKLEQKRSDRHNLLQACKMQDIKLPLSKGTMDDISQEEGSSQGE
DSVSGSQRISSIYAREALIEIDYGDLCEDLKDAQAEEEIKQEMNTLQQKLNEQQSVLQRI
AAPNMKAMEKLESVRDKFQETSDEFEAARKRAKKAKQAFEQIKKERFDRFNACFESVATN
IDEIYKALSRNSSAQAFLGPENPEEPYLDGINYNCVAPGKRFRPMDNLSGGEKTVAALAL
LFAIHSYKPAPFFVLDQIDAALDNTNIGKVANYIKEQSTCNFQAIVISLKEEFYTKAESL
IGVYPEQGDCVISKVLTFDLTKYPDANPNPNEQ

Sequence of entity 2 (B), FASTA

>6WGE_2 Structural maintenance of chromosomes protein 3 (chains B)
MYIKQVIIQGFRSYRDQTIVDPFSSKHNVIVGRNGSGKSNFFYAIQFVLSDEFSHLRPEQ
RLALLHEGTGPRVISAFVEIIFDNSDNRLPIDKEEVSLRRVIGAKKDQYFLDKKMVTKND
VMNLLESAGFSRSNPYYIVKQGKINQMATAPDSQRLKLLREVAGTRVYDERKEESISLMK
ETEGKREKINELLKYIEERLHTLEEEKEELAQYQKWDKMRRALEYTIYNQELNETRAKLD
ELSAKRETSGEKSRQLRDAQQDARDKMEDIERQVRELKTKISAMKEEKEQLSAERQEQIK
QRTKLELKAKDLQDELAGNSEQRKRLLKERQKLLEKIEEKQKELAETEPKFNSVKEKEER
GIARLAQATQERTDLYAKQGRGSQFTSKEERDKWIKKELKSLDQAINDKKRQIAAIHKDL
EDTEANKEKNLEQYNKLDQDLNEVKARVEELDRKYYEVKNKKDELQSERNYLWREENAEQ
QALAAKREDLEKKQQLLRAATGKAILNGIDSINKVLDHFRRKGINQHVQNGYHGIVMNNF
ECEPAFYTCVEVTAGNRLFYHIVDSDEVSTKILMEFNKMNLPGEVTFLPLNKLDVRDTAY
PETNDAIPMISKLRYNPRFDKAFKHVFGKTLICRSMEVSTQLARAFTMDCITLEGDQVSH
RGALTGGYYDTRKSRLELQKDVRKAEEELGELEAKLNENLRRNIERINNEIDQLMNQMQQ
IETQQRKFKASRDSILSEMKMLKEKRQQSEKTFMPKQRSLQSLEASLHAMESTRESLKAE
LGTDLLSQLSLEDQKRVDALNDEIRQLQQENRQLLNERIKLEGIITRVETYLNENLRKRL
DQVEQELNELRETEGGTVLTATTSELEAINKRVKDTMARSEDLDNSIDKTEAGIKELQKS
MERWKNMEKEHMDAINHDTKELEKMTNRQGMLLKKKEECMKKIRELGSLPQEAFEKYQTL
SLKQLFRKLEQCNTELKKYSHVNKKALDQFVNFSEQKEKLIKRQEELDRGYKSIMELMNV
LELRKYEAIQLTFKQVSKNFSEVFQKLVPGGKATLVMKKGDVEGSQSQDEGEGSGESERG
SGSQSSVPSVDQFTGVGIRVSFTGKQGEMREMQQLSGGQKSLVALALIFAIQKCDPAPFY
LFDQIDQALDAQHRKAVSDMIMELAVHAQFITTTFRPELLESADKFYGVKFRNKVSHIDV
ITAEMAKDFVEDDTTHG

Sequence of entity 3 (C), FASTA

>6WGE_3 Double-strand-break repair protein rad21 homolog (chains C)
MFYAHFVLSKRGPLAKIWLAAHWDKKLTKAHVFECNLESSVESIISPKVKMALRTSGHLL
LGVVRIYHRKAKYLLADCNEAFIKIKMAFRPGVVDLPEENREAAYNAITLPEEFHDFDQP
LPDLDDIDVAQQFSLNQSRVEEITMREEVGNISILQENDFGDFGMDDREIMAEGSAFEDD
DMLVSTTTSNLLLESEQSTSNLNEKINHLEYEDQYKDDNFGEGNDGGILDDKLISNNDGG
IFDDPPALSEAGVMLPEQPAHDDMDEDDNVSMGGPDSPASVDPVEPMPTMTDQTTLVPNE
EEAFALEPIDITVKETKAKRKRKLIVDSVKELDSKTIRAQLSDYSDIVTTLDLAPPTKKL
MMWKETGGVEKLFSLPAQPLWNNRLLKLFTRCLTPLVPEDLRKRRKGGEADNLDEFLKEF
ENPEVPREDQQQQHQQRDVIDEPIIEEPSALQESVMEASRTNIDESAMPPPPPQGVKRKA
GQIDPEPVMPPQQVEQMEIPPVELPPEEPPNICQLIPELELLPEKEKEKEKEKEDDEEEE
DEDASGGDQDQEERRWNKRTQQMLHGLQRALAKTGAESISLLELCRNTNRKQAAAKFYSF
LVLKKQQAIELTQEEPYSDIIATPGPRFHII

Sequence of entity 4 (E), FASTA

>6WGE_4 Nipped-B-like protein (chains E)
PSLSEVARKMKKKEKQKKRKAYEPKLTPEEMMDSSTFKRFTASIENILDNLEDMDFTAFG
DDDEIPQELLLGKHQLNELGSESAKIKAMGIMDKLSTDKTVKVLNILEKNIQDGSKLSTL
LNHNNDTEEEERLWRDLIMERVTKSADACLTTINIMTSPNMPKAVYIEDVIERVIQYTKF
HLQNTLYPQYDPVYRLDPHGGGLLSSKAKRAKCSTHKQRVIVMLYNKVCDIVSSLSELLE
IQLLTDTTILQVSSMGITPFFVENVSELQLCAIKLVTAVFSRYEKHRQLILEEIFTSLAR
LPTSKRSLRNFRLNSSDMDGEPMYIQMVTALVLQLIQCVVHLPSSEKDSNAEEDSNKKID
QDVVITNSYETAMRTAQNFLSIFLKKCGSKQGEEDYRPLFENFVQDLLSTVNKPEWPAAE
LLLSLLGRLLVHQFSNKSTEMALRVASLDYLGTVAARLRKDAVTSKMDQGSIERILKQVS
GGEDEIQQLQKALLDYLDENTETDPSLVFSRKFYIAQWFRDTTLETEKAMKSQKDEESSE
GTHHAKEIETTGQIMHRAENRKKFLRSIIKTTPSQFSTLKMNSDTVDYDDACLIVRYLAS
MRPFAQSFDIYLTQILRVLGENAIAVRTKAMKCLSEVVAVDPSILARLDMQRGVHGRLMD
NSTSVREAAVELLGRFVLCRPQLAEQYYDMLIERILDTGISVRKRVIKILRDICIEQPTF
PKITEMCVKMIRRVNDEEGIKKLVNETFQKLWFTPTPHNDKEAMTRKILNITDVVAACRD
TGYDWFEQLLQNLLKSEEDSSYKPVKKACTQLVDNLVEHILKYEESLADSDNKGVNSGRL
VACITTLFLFSKIRPQLMVKHAMTMQPYLTTKCSTQNDFMVICNVAKILELVVPLMEHPS
ETFLATIEEDLMKLIIKYGMTVVQHCVSCLGAVVNKVTQNFKFVWACFNRYYGAISKLKS
QHQEDPNNTSLLTNKPALLRSLFTVGALCRHFDFDLEDFKGNSKVNIKDKVLELLMYFTK
HSDEEVQTKAIIGLGFAFIQHPSLMFEQEVKNLYNNILSDKNSSVNLKIQVLKNLQTYLQ
EEDTRMQQADRDWKKVAKQEDLKEMGDVSSGMSSSIMQLYLKQVLEAFFHTQSSVRHFAL
NVIALTLNQGLIHPVQCVPYLIAMGTDPEPAMRNKADQQLVEIDKKYAGFIHMKAVAGMK
MSYQVQQAINTCLKDPVRGFRQDESSSALCSHLYSMIRGNRQHRRAFLISLLNLFDDTAK
TDVTMLLYIADNLACFPYQTQEEPLFIMHHIDITLSVSGSNLLQSFKESMVKDKRKERKS
SPSKENESSDSEEEVSRPRKSRKRVDSDSDSDSEDDINSVMKCLPENSAPLIEFANVSQG
ILLLLMLKQHLKNLCGFSDSKIQKYSPSESAKVYDKAINRKTGVHFHPKQTLDFLRSDMA
NSKITEEVKRSIVKQYLDFKLLMEHLDPDEEEEEGEVSASTNARNKAITSLLGGGSPKNN
TAAETEDDESDGEDRGGGTSGSLRRSKRNSDSTELAAQMNESVDVMDVIAICCPKYKDRP
QIARVVQKTSSGFSVQWMAGSYSGSWTEAKRRDGRKLVPWVDTIKESDIIYKKIALTSAN
KLTNKVVQTLRSLYAAKDGTSS

Sequence of entity 5 (F), FASTA

>6WGE_5 DNA (43-MER) (chains F)
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA

Sequence of entity 6 (G), FASTA

>6WGE_6 DNA (43-MER) (chains G)
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	2
ANP	Phosphoaminophosphonic acid-adenylate ester	C10 H17 N6 O12 P3	2

Primary citation

Cryo-EM structure of the human cohesin-NIPBL-DNA complex. Shi, Z., Gao, H., Bai, X.C. et al. Science (2020) 368:1454-1459. DOI 10.1126/science.abb0981 · PubMed

Other PDB entries of the same protein (UniProt Q14683 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8ROE 1.36 Å, Human cohesin SMC1A-HD(shortCC-EQ)/RAD21-C complex - ADP-bound conformation
8ROD 1.5 Å, Human cohesin SMC1A-HD(shortCC-EQ)/RAD21-C complex - Open/closed P-loop conformation
8ROF 1.65 Å, Human cohesin SMC1A-HD(shortCC-EQ)/RAD21-C complex - ADP-Mg-bound conformation
8RO9 1.77 Å, Human cohesin SMC1A-HD(longCC-EQ)/RAD21-C complex - Open/closed P-loop conformation
8ROC 1.85 Å, Human cohesin SMC1A-HD(shortCC-EQ)/RAD21-C complex - Apo closed P-loop conformation
8RO8 1.9 Å, Human cohesin SMC1A-HD(longCC-EQ)/RAD21-C complex - Apo closed P-loop conformation
8ROG 1.94 Å, Human cohesin SMC1A-HD(shortCC-EQ)/RAD21-C complex - ATPgS-Mg-bound conformation
8RO7 2.09 Å, Human cohesin SMC1A-HD(longCC)/RAD21-C complex - Open/closed P-loop conformation
8RO6 2.2 Å, Human cohesin SMC1A-HD(longCC)/RAD21-C complex - Apo closed P-loop conformation
6WG4 2.31 Å, Crystal structure of human SMC1-SMC3 hinge domain heterodimer in south-open conformation
8ROA 2.44 Å, Human cohesin SMC1A-HD(longCC-EQ)/RAD21-C complex - ADP-bound conformation
8ROB 2.5 Å, Human cohesin SMC1A-HD(longCC-EQ)/RAD21-C complex - ATPgS-Mg-bound conformation

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