8PQ5: Structural maintenance of chromosomes protein 1A

Human Cohesin ATPase module with an open DNA exit gate. Determined by electron microscopy at 4.4 Å resolution. Released 11 Sept 2024.

Method: Electron microscopy
Resolution: 4.4 Å
Organism: Homo sapiens
Chains: 3
Atoms: 6,300
Mol. weight: 114.05 kDa
Ligands: ATP
Released: 11 Sept 2024

Explore 8PQ5 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8PQ5 contains 32 α-helices and 34 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 A: 12 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	4-10	7	1
β-strand	12	1	2
β-strand	15	1	2
β-strand	20-21	2	1
β-strand	27-30	4	3
α-helix	38-48	11
α-helix	68-70	3
β-strand	77	1	1
β-strand	79-84	6	1
β-strand	92-99	8	1
β-strand	102-107	6	1
β-strand	111-112	2	1
α-helix	114-121	8
α-helix	122-124	3
α-helix	139-141	3
α-helix	148-157	10
α-helix	162-164	3
α-helix	165-180	16
α-helix	1053-1089	37
β-strand	1095-1099	5	4
β-strand	1112-1116	5	4
α-helix	1130-1132	3
α-helix	1133-1146	14
β-strand	1152-1154	3	3
α-helix	1164-1175	12
β-strand	1183-1187	5	3
β-strand	1200-1201	2	3
β-strand	1202-1206	5	5
β-strand	1212-1216	5	5

Chain B: 17 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	6
α-helix	21-23	3
β-strand	27-32	6	7
α-helix	38-49	12
α-helix	51-53	3
α-helix	60-63	4
α-helix	72-73	2
β-strand	76-82	7	6
β-strand	97-102	6	6
β-strand	109-111	3	6
β-strand	115-116	2	6
α-helix	119-127	9
β-strand	138	1	7
α-helix	143-146	4
α-helix	152-163	12
α-helix	166-181	16
α-helix	183-192	10
α-helix	1006-1047	42
β-strand	1054-1057	4	8
β-strand	1096-1099	4	8
β-strand	1100	1	9
β-strand	1110	1	9
α-helix	1112-1114	3
α-helix	1120-1134	15
β-strand	1139-1141	3	7
α-helix	1151-1164	14
β-strand	1169-1171	3	7
α-helix	1177-1180	4
β-strand	1185-1192	8	7
β-strand	1195-1199	5	7
α-helix	1200-1202	3
α-helix	1203-1209	7

Chain C: 3 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	559-562	4
α-helix	590-602	13
α-helix	603-606	4
β-strand	609	1	10
β-strand	624	1	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Structural maintenance of chromosomes protein 1A	A	protein	456	Homo sapiens	Q14683 (AlphaFold model)
Structural maintenance of chromosomes protein 3	B	protein	462	Homo sapiens	Q9UQE7 (AlphaFold model)
64-kDa C-terminal product	C	protein	81	Homo sapiens	O60216 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>8PQ5_1 Structural maintenance of chromosomes protein 1A (chains A)
MGFLKLIEIENFKSYKGRQIIGPFQRFTAIIGPNGSGKSNLMDAISFVLGEKTSNLRVKT
LRDLIHGAPVGKPAANRAFVSMVYSEEGAEDRTFARVIVGGSSEYKINNKVVQLHEYSEE
LEKLGILIKARNFLVFQGAVESIAMKNPKERTALFEEISRSGELAQEYDKRKKEMVKAEE
DTQFNYHRKKNIAAERKEAKESSKHPTSLVPRGSDAQAEEEIKQEMNTLQQKLNEQQSVL
QRIAAPNMKAMEKLESVRDKFQETSDEFEAARKRAKKAKQAFEQIKKERFDRFNACFESV
ATNIDEIYKALSRNSSAQAFLGPENPEEPYLDGINYNCVAPGKRFRPMDNLSGGEKTVAA
LALLFAIHSYKPAPFFVLDQIDAALDNTNIGKVANYIKEQSTCNFQAIVISLKEEFYTKA
ESLIGVYPEQGDCVISKVLTFDLTKYPDANPNPNEQ

Sequence of entity 2 (B), FASTA

>8PQ5_2 Structural maintenance of chromosomes protein 3 (chains B)
MYIKQVIIQGFRSYRDQTIVDPFSSKHNVIVGRNGSGKSNFFYAIQFVLSDEFSHLRPEQ
RLALLHEGTGPRVISAFVEIIFDNSDNRLPIDKEEVSLRRVIGAKKDQYFLDKKMVTKND
VMNLLESAGFSRSNPYYIVKQGKINQMATAPDSQRLKLLREVAGTRVYDERKEESISLMK
ETEGKREKINELLKYIEERLHTLEEEKEELAGSGSLVPRGSGSYSHVNKKALDQFVNFSE
QKEKLIKRQEELDRGYKSIMELMNVLELRKYEAIQLTFKQVSKNFSEVFQKLVPGGKATL
VMKKGDVEGSQSQDEGEGSGESERGSGSQSSVPSVDQFTGVGIRVSFTGKQGEMREMQQL
SGGQKSLVALALIFAIQKCDPAPFYLFDQIDQALDAQHRKAVSDMIMELAVHAQFITTTF
RPELLESADKFYGVKFRNKVSHIDVITAEMAKDFVEDDTTHG

Sequence of entity 3 (C), FASTA

>8PQ5_3 64-kDa C-terminal product (chains C)
MKRTQQMLHGLQRALAKTGAESISLLELCRNTNRKQAAAKFYSFLVLKKQQAIELTQEEP
YSDIIATPGPRFHGSLEVLFQ

Ligands and cofactors

ID	Name	Formula	Copies
ATP	Adenosine-5'-triphosphate	C10 H16 N5 O13 P3	2

Primary citation

The cohesin ATPase cycle is mediated by specific conformational dynamics and interface plasticity of SMC1A and SMC3 ATPase domains. Vitoria Gomes, M., Landwerlin, P., Diebold-Durand, M.L. et al. Cell Rep (2024) 43:114656-114656. DOI 10.1016/j.celrep.2024.114656 · 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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