6QNX: SA2/SCC1/CTCF complex

Structure of the SA2/SCC1/CTCF complex. Determined by X-ray diffraction at 2.7 Å resolution. Released 22 Jan 2020.

Method: X-ray diffraction
Resolution: 2.7 Å
Organism: Homo sapiens
Chains: 3
Atoms: 8,229
Mol. weight: 130.89 kDa
Released: 22 Jan 2020

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

Secondary structure: helices and β-sheets

6QNX contains 63 α-helices and 8 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: 58 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	81-89	9
α-helix	95-108	14
α-helix	110-124	15
α-helix	133-138	6
α-helix	141-151	11
α-helix	160-162	3
α-helix	166-185	20
α-helix	190-192	3
α-helix	196-207	12
β-strand	212	1	1
α-helix	213-252	40
α-helix	261-288	28
α-helix	289-293	5
α-helix	294-296	3
β-strand	299	1	2
α-helix	302-318	17
α-helix	320-323	4
α-helix	326-335	10
α-helix	341-356	16
α-helix	363-377	15
α-helix	378-380	3
β-strand	381	1	3
α-helix	384-400	17
α-helix	407-415	9
α-helix	416-418	3
β-strand	419	1	4
α-helix	422-436	15
α-helix	458-470	13
α-helix	478-483	6
α-helix	489-492	4
α-helix	495-501	7
α-helix	515-533	19
α-helix	537-538	2
α-helix	550-577	28
α-helix	582-588	7
α-helix	592-594	3
α-helix	598-602	5
α-helix	606-621	16
α-helix	626-639	14
α-helix	647-672	26
α-helix	681-700	20
α-helix	704-706	3
α-helix	709-722	14
α-helix	727-747	21
α-helix	757-775	19
α-helix	781-797	17
α-helix	800-802	3
α-helix	808-810	3
α-helix	816-818	3
α-helix	819-832	14
α-helix	851-873	23
α-helix	879-882	4
α-helix	883-886	4
α-helix	893-910	18
α-helix	912-933	22
α-helix	943-957	15
α-helix	967-981	15
α-helix	999-1003	5
α-helix	1004-1009	6
α-helix	1014-1025	12
α-helix	1028-1032	5
α-helix	1039-1045	7

Chain B: 4 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	326	1	1
β-strand	331	1	2
α-helix	334-342	9
β-strand	348	1	3
β-strand	353	1	4
α-helix	358-365	8
α-helix	369-372	4
α-helix	383-390	8

Chain C: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	224-226	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Cohesin subunit SA-2	A	protein	981	Homo sapiens	Q8N3U4 (AlphaFold model)
64-kDa C-terminal product	B	protein	140	Homo sapiens	O60216 (AlphaFold model)
Transcriptional repressor CTCF	C	protein	10	Homo sapiens	P49711 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6QNX_1 Cohesin subunit SA-2 (chains A)
ENMMLFEVVKMGKSAMQSVVDDWIESYKHDRDIALLDLINFFIQCSGCKGVVTAEMFRHM
QNSEIIRKMTEEFDEDSGDYPLTMAGPQWKKFKSSFCEFIGVLVRQCQYSIIYDEYMMDT
VISLLTGLSDSQVRAFRHTSTLAAMKLMTALVNVALNLSINMDNTQRQYEAERNKMIGKR
ANERLELLLQKRKELQENQDEIENMMNAIFKGVFVHRYRDAIAEIRAICIEEIGIWMKMY
SDAFLNDSYLKYVGWTMHDKQGEVRLKCLTALQGLYYNKELNSKLELFTSRFKDRIVSMT
LDKEYDVAVQAIKLLTLVLQSSEEVLTAEDCENVYHLVYSAHRPVAVAAGEFLYKKLFSR
RDPEEDGMMKRRGRQGPNANLVKTLVFFFLESELHEHAAYLVDSMWDCATELLKDWECMN
SLLLEEPLSGEEALTDRQESALIEIMLCTIRQAAECHPPVGRGTGKRVLTAKEKKTQLDD
RTKITELFAVALPQLLAKYSVDAEKVTNLLQLPQYFDLEIYTTGRLEKHLDALLRQIRNI
VEKHTDTDVLEACSKTYHALCNEEFTIFNRVDISRSQLIDELADKFNRLLEDFLQEGEEP
DEDDAYQVLSTLKRITAFHNAHDLSKWDLFACNYKLLKTGIENGDMPEQIVIHALQCTHY
VILWQLAKITESSSTKEDLLRLKKQMRVFCQICQHYLTNVNTTVKEQAFTILCDILMIFS
HQIMSGGRDMLEPLVYTPDSSLQSELLSFILDHVFIEQDDDNNSADGQQEDEASKIEALH
KRRNLLAAFCKLIVYTVVEMNTAADIFKQYMKYYNDYGDIIKETMSKTRQIDKIQCAKTL
ILSLQQLFNEMIQENGYNFDRSSSTFSGIKELARRFALTFGLDQLKTREAIAMLHKDGIE
FAFKEPNPQGESHPPLNLAFLDILSEFSSKLLRQDKRTVYVYLEKFMTFQMSLRREDVWL
PLMSYRNSLLAGGDDDTMSVI

Sequence of entity 2 (B), FASTA

>6QNX_2 64-kDa C-terminal product (chains B)
VDPVEPMPTMTDQTTLVPNEEEAFALEPIDITVKETKAKRKRKLIVDSVKELDSKTIRAQ
LSDYSDIVTTLDLAPPTKKLMMWKETGGVEKLFSLPAQPLWNNRLLKLFTRCLTPLVPED
LRKRRKGGEADNLDEFLKEF

Sequence of entity 3 (C), FASTA

>6QNX_3 Transcriptional repressor CTCF (chains C)
DVSVYDFEEE

Primary citation

The structural basis for cohesin-CTCF-anchored loops. Li, Y., Haarhuis, J.H.I., Sedeno Cacciatore, A. et al. Nature (2020) 578:472-476. DOI 10.1038/s41586-019-1910-z · PubMed

Other PDB entries of the same protein (UniProt Q8N3U4 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4PJW 2.85 Å, crystal structure of human Stromal Antigen 2 (SA2) in complex with Sister Chromatid…
9HMV 2.9 Å, Cryo-EM structure of SA2-SCC1 complex at 2.9 angstrom
4PK7 2.95 Å, crystal structure of human Stromal Antigen 2 (SA2) in complex with Sister Chromatid…
4PJU 3.05 Å, crystal structure of human Stromal Antigen 2 (SA2) in complex with Sister Chromatid…
9HX9 3.07 Å, Structure of the SA2/SCC1/MCM3 complex
9EP3 3.08 Å, Structure of the SA2/SCC1/WAPL complex
7ZJS 3.24 Å, Structural basis of centromeric cohesion protection by SGO1
9HMS 3.4 Å, Cryo-EM structure of human separase bound to SCC1 (310-550 aa) and SA2
8K4D 3.52 Å, Structure of the SA2/Scc1/CENP_U complex

Browse structure collections

About this viewer

MolViewer shows 6QNX 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.