4JGH: SOCS2-Elongin BC complex

Name: PDB 4JGH: Structure of the SOCS2-Elongin BC complex bound to an N-terminal fragment of Cullin5
Published: 2013-08-07
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ligase

Structure of the SOCS2-Elongin BC complex bound to an N-terminal fragment of Cullin5. Determined by X-ray diffraction at 3.0 Å resolution. Released 7 Aug 2013.

Method: X-ray diffraction
Resolution: 3.0 Å
Organisms: Homo sapiens, Mus musculus
Chains: 4
Atoms: 5,902
Mol. weight: 87.88 kDa
Released: 7 Aug 2013

Explore 4JGH in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4JGH contains 44 α-helices and 21 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: 8 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	29-39	11
α-helix	42-45	4
β-strand	49	1	1
α-helix	55-63	9
α-helix	66	1
β-strand	69-74	6	1
β-strand	82-88	7	1
β-strand	91-100	10	1
β-strand	103-106	4	1
β-strand	119	1	1
α-helix	122-134	13
β-strand	154-155	2	1
α-helix	163-174	12
α-helix	178-180	3
α-helix	187-190	4

Chain B: 7 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	2-8	7	2
β-strand	12-19	8	2
β-strand	23	1	3
α-helix	24-35	12
α-helix	39-41	3
β-strand	42-45	4	2
β-strand	50	1	2
α-helix	51-52	2
β-strand	56	1	3
β-strand	68	1	4
β-strand	71	1	4
α-helix	72	1
β-strand	73-79	7	2
β-strand	80	1	5
β-strand	85	1	5
α-helix	86-87	2
α-helix	91-100	10
α-helix	101-103	3

Chain C: 6 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	18-22	5	2
β-strand	28-32	5	2
α-helix	33-36	4
α-helix	40-45	6
α-helix	48-50	3
α-helix	57	1
β-strand	58-61	4	2
α-helix	67-81	15
α-helix	100-110	11

Chain D: 23 helices, 0 β-strands

Element	Residues	Length
α-helix	15-30	16
α-helix	37-53	17
α-helix	57-81	25
α-helix	86-103	18
α-helix	109-111	3
α-helix	112-115	4
α-helix	134-143	10
α-helix	144-148	5
α-helix	149-167	19
α-helix	175-186	12
α-helix	196-197	2
α-helix	198-203	6
α-helix	204-224	21
α-helix	227-248	22
α-helix	257-269	13
α-helix	271-273	3
α-helix	274-277	4
α-helix	278-280	3
α-helix	281-286	6
α-helix	290-300	11
α-helix	310-333	24
α-helix	337-357	21
α-helix	363-377	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Suppressor of cytokine signaling 2	A	protein	173	Homo sapiens	O14508 (AlphaFold model)
Transcription elongation factor B polypeptide 2	B	protein	118	Mus musculus	P62869 (AlphaFold model)
Transcription elongation factor B polypeptide 1	C	protein	96	Mus musculus	P83940 (AlphaFold model)
Cullin-5	D	protein	378	Homo sapiens	Q93034 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>4JGH_1 Suppressor of cytokine signaling 2 (chains A)
HMDPEFQAARLAKALRELGQTGWYWGSMTVNEAKEKLKEAPEGTFLIRDSSHSDYLLTIS
VKTSAGPTNLRIEYQDGKFRLDSIICVKSKLKQFDSVVHLIDYYVQMCKDKRTGPEAPRN
GTVHLYLTKPLYTSAPSLQHLCRLTINKCTGAIWGLPLPTRLKDYLEEYKFQV

Sequence of entity 2 (B), FASTA

>4JGH_2 Transcription elongation factor B polypeptide 2 (chains B)
MDVFLMIRRHKTTIFTDAKESSTVFELKRIVEGILKRPPEEQRLYKDDQLLDDGKTLGEC
GFTSQTARPQAPATVGLAFRADDTFEALRIEPFSSPPELPDVMKPQDSGGSANEQAVQ

Sequence of entity 3 (C), FASTA

>4JGH_3 Transcription elongation factor B polypeptide 1 (chains C)
MYVKLISSDGHEFIVKREHALTSGTIKAMLSGPGQFAENETNEVNFREIPSHVLSKVCMY
FTYKVRYTNSSTEIPEFPIAPEIPLELLMAANFLDC

Sequence of entity 4 (D), FASTA

>4JGH_4 Cullin-5 (chains D)
KGSLQFEDKWDFMRPIVLKLLRQESVTKQQWFDLFSDVHAVCLWDDKGPAKIHQALKEDI
LEFIKQAQARVLSHQDDTALLKAYIVEWRKFFTQCDILPKPFCQLEITLMGKQGSNKKSN
VEDSIVRKLMLDTWNESIFSNIKNRLQDSAMKLVHAERLGEAFDSQLVIGVRESYVNLCS
NPEDKLQIYRDNFEKAYLDSTERFYRTQAPSYLQQNGVQNYMKYADAKLKEEEKRALRYL
ETRRECNSVEALMECCVNALVTSFKETILAECQGMIKRNETEKLHLMFSLMDKVPNGIEP
MLKDLEEHIISAGLADMVAAAETITTDSEKYREQLDTLFNRFSKLVKEAFQDDPRFLTAR
DKAYKAVVNDATIFKLEV

Primary citation

Structural basis of intersubunit recognition in elongin BC-cullin 5-SOCS box ubiquitin-protein ligase complexes. Kim, Y.K., Kwak, M.J., Ku, B. et al. Acta Crystallogr D Biol Crystallogr (2013) 69:1587-1597. DOI 10.1107/S0907444913011220 · PubMed

Other PDB entries of the same protein (UniProt O14508 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7ZLM 1.79 Å, Crystal structure of SOCS2:ElonginB:ElonginC in complex with compound MN551
2C9W 1.9 Å, Crystal structure of socs-2 in complex with elongin-B and elongin-C at 1.9A resolution
7ZLS 1.92 Å, co-crystal structure of SOCS2:ElonginB:ElonginC in complex with compound 13
7ZLP 1.94 Å, Crystal structure of SOCS2:ElonginB:ElonginC in complex with compound 9
6I5N 1.98 Å, Crystal structure of SOCS2:Elongin C:Elongin B in complex with growth hormone receptor…
7ZLR 2.01 Å, Crystal structure of SOCS2:ElonginB:ElonginC in complex with compound 13
7ZLO 2.22 Å, Crystal structure of SOCS2:ElonginB:ElonginC in complex with compound 12
7ZLN 2.6 Å, Crystal structure of SOCS2:ElonginB:ElonginC in complex with compound 11
6I4X 2.69 Å, Crystal structure of SOCS2:Elongin C:Elongin B in complex with erythropoietin receptor…
6I5J 2.8 Å, Crystal structure of SOCS2:Elongin C:Elongin B in complex with growth hormone receptor…
5BO4 2.9 Å, Structure of SOCS2:Elongin C:Elongin B from DMSO-treated crystals
7M6T 3.19 Å, Crystal structure of SOCS2/ElonginB/ElonginC bound to a non-canonical peptide that…

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