Research workbench

Cryo-EM structure of a membrane PROTEIN(WT)

Analyse Cryo-EM structure of a membrane PROTEIN(WT) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7FJD
Type: protein
Length: 1,058 residues
Chains: 8
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: T-cell surface glycoprotein CD3 zeta chain; T-cell surface glycoprotein CD3 delta chain…
UniProt: P20963, P04234, P07766, P09693, A0A0B4J271, A0N4Z6, P01848, A0A0K0K1A5, P0DSE2, A0A0G2JMB4
Ligands: CLR
Pockets: 15 · best druggability 0.84

Structure

electron microscopy · 8 distinct chains · 23% helix, 32% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
a	T-cell surface glycoprotein CD3 zeta chain	protein	33	73% helix, 0% strand	P20963
b	T-cell surface glycoprotein CD3 zeta chain	protein	29	83% helix, 0% strand	P20963
d	T-cell surface glycoprotein CD3 delta chain	protein	107	27% helix, 31% strand	P04234
e	T-cell surface glycoprotein CD3 epsilon chain	protein	123	24% helix, 31% strand	P07766
f	T-cell surface glycoprotein CD3 epsilon chain	protein	120	22% helix, 33% strand	P07766
g	T-cell surface glycoprotein CD3 gamma chain	protein	113	26% helix, 40% strand	P09693
m	T cell receptor alpha variable 12-3,POSSIBLE J 11 gene SEGMENT,T cell receptor alpha chain constant	protein	246	14% helix, 32% strand	A0A0B4J271, A0N4Z6, P01848
n	T cell receptor beta variable 6-5,M1-specific T cell receptor beta CHAIN,T cell receptor beta constant 2	protein	287	18% helix, 38% strand	A0A0K0K1A5, P0DSE2, A0A0G2JMB4

Ligands and binding sites

CLR · Cholesterol · ligand · 2 copies · chains b, g, n, m

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

15 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1098	0.84	0.85	104	empty
2	873	0.84	0.85	67	CLR
3	1034	0.71	0.75	87	empty
4	374	0.66	0.80	47	empty
5	399	0.63	0.77	24	empty

Interfaces

21 interfaces between chains.

m–n · 3743 Å² buried · 20 hydrogen bonds · protein-protein
f–g · 1640 Å² buried · 19 hydrogen bonds · protein-protein
d–e · 1639 Å² buried · 20 hydrogen bonds · protein-protein
d–m · 1142 Å² buried · 9 hydrogen bonds · protein-protein
g–n · 763 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 13 disulfide (disulfide).

Compared structures

7FJD · Cryo-EM structure of a membrane protein(WT) · the same entry in another collection · chain n against n, TM-score 1.00
P0DSE2 · AlphaFold monomer V2.0 prediction for M1-specific T cell receptor beta chain (P0DSE2) · a predicted model of the same protein · chain n against A, TM-score 0.93
P07766 · AlphaFold monomer V2.0 prediction for T-cell surface glycoprotein CD3 epsilon chain… · a predicted model of the same protein · chain f against A, TM-score 0.84
P20963 · P20963 · a predicted model of the same protein · chain b against A, TM-score 0.78

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P20963
Every structure of UniProt P04234
Every structure of UniProt P07766
Every structure of UniProt P09693
Every structure of UniProt A0A0B4J271
Every structure of UniProt A0N4Z6
Every structure of UniProt P01848
Every structure of UniProt A0A0K0K1A5
Every structure of UniProt P0DSE2
Every structure of UniProt A0A0G2JMB4
Elsewhere: RCSB PDB 7FJD · PDBe 7FJD · UniProt P20963 · UniProt P04234 · UniProt P07766 · UniProt P09693 · UniProt A0A0B4J271 · UniProt A0N4Z6 · UniProt P01848 · UniProt A0A0K0K1A5 · UniProt P0DSE2 · UniProt A0A0G2JMB4

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