7FJD: Membrane protein(WT)

Cryo-EM structure of a membrane protein(WT). Determined by electron microscopy at 3.2 Å resolution. Released 27 Jul 2022.

Method: Electron microscopy
Resolution: 3.2 Å
Organism: Homo sapiens
Chains: 8
Atoms: 8,352
Mol. weight: 189.56 kDa
Ligands: CLR
Released: 27 Jul 2022

Explore 7FJD in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7FJD contains 19 α-helices and 77 β-strands across 8 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.

Chains a and b: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	30-53	24

Chain d: 3 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	26-27	2	1
β-strand	32-36	5	1
β-strand	42-46	5	2
β-strand	51	1	1
β-strand	57-62	6	1
α-helix	63-65	3
β-strand	68-72	5	2
α-helix	77-79	3
β-strand	85-91	7	2
β-strand	97-98	2	3
α-helix	103-125	23

Chain e: 2 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	37-40	4	4
β-strand	44-48	5	4
β-strand	57-61	5	2
β-strand	65-66	2	2
β-strand	75-77	3	4
β-strand	81-85	5	4
β-strand	95-100	6	2
α-helix	105-107	3
β-strand	111-116	6	2
β-strand	122-123	2	3
α-helix	127-153	27

Chain f: 3 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	37-41	5	5
β-strand	44-48	5	5
β-strand	57-61	5	6
β-strand	75-76	2	5
β-strand	81-85	5	5
β-strand	94-100	7	6
α-helix	105-107	3
β-strand	111-117	7	6
β-strand	122-124	3	7
α-helix	129-141	13
α-helix	144-153	10

Chain g: 2 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	31-34	4	8
β-strand	41-46	6	8
β-strand	53-57	5	6
β-strand	60-65	6	6
β-strand	71-76	6	8
α-helix	77-79	3
β-strand	82-88	7	6
β-strand	93	1	6
β-strand	97-103	7	6
β-strand	107-109	3	7
α-helix	112-137	26

Chain m: 2 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	33-36	4	9
β-strand	41-46	6	10
β-strand	54-60	7	11
β-strand	67-72	6	11
β-strand	83-88	6	10
β-strand	93-98	6	10
β-strand	108-114	7	11
β-strand	121-122	2	11
β-strand	126-127	2	11
β-strand	128-131	4	9
β-strand	140-143	4	12
β-strand	153-158	6	12
β-strand	174-176	3	12
β-strand	180-184	5	13
β-strand	189-193	5	13
β-strand	195-198	4	12
β-strand	219	1	12
α-helix	232-234	3
α-helix	241-272	32

Chain n: 5 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	24-26	3	14
β-strand	29-33	5	15
β-strand	38-40	3	16
β-strand	41-43	3	14
β-strand	51-56	6	15
β-strand	63-70	8	15
β-strand	73-76	4	15
β-strand	83-85	3	16
β-strand	92	1	14
β-strand	95-97	3	16
α-helix	102-104	3
β-strand	106-109	4	15
β-strand	112	1	15
β-strand	129-133	5	15
β-strand	140	1	17
β-strand	143-147	5	18
α-helix	148-150	3
α-helix	151-156	6
β-strand	159-169	11	18
β-strand	170	1	17
β-strand	174-180	7	19
β-strand	183-184	2	19
β-strand	189-191	3	18
β-strand	196-197	2	18
β-strand	207-216	10	18
α-helix	217-220	4
β-strand	226-233	8	19
β-strand	236	1	20
β-strand	250	1	20
β-strand	252-259	8	19
α-helix	270-307	38

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
T-cell surface glycoprotein CD3 zeta chain	a, b	protein	165	Homo sapiens	P20963 (AlphaFold model)
T-cell surface glycoprotein CD3 delta chain	d	protein	171	Homo sapiens	P04234 (AlphaFold model)
T-cell surface glycoprotein CD3 epsilon chain	e, f	protein	207	Homo sapiens	P07766 (AlphaFold model)
T-cell surface glycoprotein CD3 gamma chain	g	protein	182	Homo sapiens	P09693 (AlphaFold model)
T cell receptor alpha variable 12-3,Possible J 11 gene segment,T cell receptor alpha chain constant	m	protein	272	Homo sapiens	A0A0B4J271, A0N4Z6, P01848
T cell receptor beta variable 6-5,M1-specific T cell receptor beta chain,T cell receptor beta…	n	protein	312	Homo sapiens	A0A0K0K1A5, P0DSE2

Sequence of entity 1 (a, b), FASTA

>7FJD_1 T-cell surface glycoprotein CD3 zeta chain (chains a, b)
MKWKALFTAAILQAQLPITEAQSFGLLDPKLCYLLDGILFIYGVILTALFLRVKFSRSAD
APAYQQGQNQLYNELNLGRREEYDVLDKRRGRDPEMGGKPQRRKNPQEGLYNELQKDKMA
EAYSEIGMKGERRRGKGHDGLYQGLSTATKDTYDALHMQALPPRS

Sequence of entity 2 (d), FASTA

>7FJD_2 T-cell surface glycoprotein CD3 delta chain (chains d)
MEHSTFLSGLVLATLLSQVSPFKIPIEELEDRVFVNCNTSITWVEGTVGTLLSDITRLDL
GKRILDPRGIYRCNGTDIYKDKESTVQVHYRMCQSCVELDPATVAGIIVTDVIATLLLAL
GVFCFAGHETGRLSGAADTQALLRNDQVYQPLRDRDDAQYSHLGGNWARNK

Sequence of entity 3 (e, f), FASTA

>7FJD_3 T-cell surface glycoprotein CD3 epsilon chain (chains e, f)
MQSGTHWRVLGLCLLSVGVWGQDGNEEMGGITQTPYKVSISGTTVILTCPQYPGSEILWQ
HNDKNIGGDEDDKNIGSDEDHLSLKEFSELEQSGYYVCYPRGSKPEDANFYLYLRARVCE
NCMEMDVMSVATIVIVDICITGGLLLLVYYWSKNRKAKAKPVTRGAGAGGRQRGQNKERP
PPVPNPDYEPIRKGQRDLYSGLNQRRI

Sequence of entity 4 (g), FASTA

>7FJD_4 T-cell surface glycoprotein CD3 gamma chain (chains g)
MEQGKGLAVLILAIILLQGTLAQSIKGNHLVKVYDYQEDGSVLLTCDAEAKNITWFKDGK
MIGFLTEDKKKWNLGSNAKDPRGMYQCKGSQNKSKPLQVYYRMCQNCIELNAATISGFLF
AEIVSIFVLAVGVYFIAGQDGVRQSRASDKQTLLPNDQLYQPLKDREDDQYSHLQGNQLR
RN

Sequence of entity 5 (m), FASTA

>7FJD_5 T cell receptor alpha variable 12-3,Possible J 11 gene segment,T cell receptor alpha chain constant (chains m)
MKSLRVLLVILWLQLSWVWSQQKEVEQDPGPLSVPEGAIVSLNCTYSNSAFQYFMWYRQY
SRKGPELLMYTYSSGNKEDGRFTAQVDKSSKYISLFIRDSQPSDSATYLCAMSKGYSTLT
FGKGTMLLVSPDIQNPDPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKTV
LDMRSMDFKSNSAVAWSNKSDFACANAFNNSIIPEDTFFPSPESSCDVKLVEKSFETDTN
LNFQNLSVIGFRILLLKVAGFNLLMTLRLWSS

Sequence of entity 6 (n), FASTA

>7FJD_6 T cell receptor beta variable 6-5,M1-specific T cell receptor beta chain,T cell receptor beta constant 2 (chains n)
MSISLLCCAALSLLWAGPVNAGVTQTPKFQVLKTGQSMTLQCAQDMNHEYMSWYRQDPGM
GLRLIHYSVGAGITDQGEVPNGYNVSRSTTEDFPLRLLSAAPSQTSVYFCASRRRQGASG
EQYFGPGTRLTVTEDLKNVFPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWV
NGKEVHSGVSTDPQPLKEQPALNDSRYCLSSRLRVSATFWQNPRNHFRCQVQFYGLSEND
EWTQDRAKPVTQIVSAEAWGRADCGFTSESYQQGVLSATILYEILLGKATLYAVLVSALV
LMAMVKRKDSRG

Ligands and cofactors

ID	Name	Formula	Copies
CLR	Cholesterol	C27 H46 O	2

Primary citation

Cholesterol inhibits TCR signaling by directly restricting TCR-CD3 core tunnel motility. Chen, Y., Zhu, Y., Li, X. et al. Mol Cell (2022) 82:1278-1287.e5. DOI 10.1016/j.molcel.2022.02.017 · PubMed

Other PDB entries of the same protein (UniProt P20963 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2OQ1 1.9 Å, Tandem SH2 domains of ZAP-70 with 19-mer zeta1 peptide
3IK5 2.05 Å, SIVmac239 Nef in complex with TCR zeta ITAM 1 polypeptide (A63-R80)
8ES8 2.65 Å, CryoEM structure of PN45545 TCR-CD3 in complex with HLA-A2 MAGEA4 (230-239)
4XZ1 2.8 Å, ZAP-70-tSH2:Compound-B adduct
1YGR 2.9 Å, Crystal structure of the tandem phosphatase domain of RPTP CD45
7FJE 3.0 Å, Cryo-EM structure of a membrane protein(LL)
9CI8 3.01 Å, T cell receptor complex
8ES7 3.04 Å, CryoEM structure of PN45545 TCR-CD3 complex
7PHR 3.08 Å, Structure of a fully assembled T-cell receptor engaging a tumor-associated peptide-MHC I
9JY1 3.08 Å, delta epsilon/delta epsilon Fab-TCR tetramer
7FJF 3.1 Å, Cryo-EM structure of a membrane protein(CS)
8TW6 3.1 Å, TCR in nanodisc ND-II

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