7fjf

Cryo-EM structure of a membrane protein(CS)

Method: ELECTRON MICROSCOPY

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1. Protein Identity and Related Structures Protein Identity & Related Structures

T-cell surface glycoprotein CD3 zeta chain

Homo sapiens

UniProt P20963

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 8	T-cell surface glycoprotein CD3 delta chain × 1 （P04234） T-cell surface glycoprotein CD3 epsilon chain × 2 （P07766） T-cell surface glycoprotein CD3 gamma chain × 1 （P09693） T cell receptor alpha variable 12-3,Possible J 11 gene segment,T cell receptor alpha chain constant × 1 （A0A0B4J271,A0N4Z6,P01848） T cell receptor beta variable 6-5,M1-specific T cell receptor beta chain,T cell receptor beta constant 2 × 1 （A0A0G2JMB4,A0A0K0K1A5,P0DSE2） CHOLEST-5-EN-3-YL HYDROGEN SULFATE × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CD3Z_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain a； PDBConstruct 1–164； UniProt 1–164 Author chain b； PDBConstruct 1–164； UniProt 1–164

T-cell surface glycoprotein CD3 delta chain

Homo sapiens

UniProt P04234

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 8	T-cell surface glycoprotein CD3 zeta chain × 2 （P20963） T-cell surface glycoprotein CD3 epsilon chain × 2 （P07766） T-cell surface glycoprotein CD3 gamma chain × 1 （P09693） T cell receptor alpha variable 12-3,Possible J 11 gene segment,T cell receptor alpha chain constant × 1 （A0A0B4J271,A0N4Z6,P01848） T cell receptor beta variable 6-5,M1-specific T cell receptor beta chain,T cell receptor beta constant 2 × 1 （A0A0G2JMB4,A0A0K0K1A5,P0DSE2） CHOLEST-5-EN-3-YL HYDROGEN SULFATE × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CD3D_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain d； PDBConstruct 1–171； UniProt 1–171

T-cell surface glycoprotein CD3 epsilon chain

Homo sapiens

UniProt P07766

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 8	T-cell surface glycoprotein CD3 zeta chain × 2 （P20963） T-cell surface glycoprotein CD3 delta chain × 1 （P04234） T-cell surface glycoprotein CD3 gamma chain × 1 （P09693） T cell receptor alpha variable 12-3,Possible J 11 gene segment,T cell receptor alpha chain constant × 1 （A0A0B4J271,A0N4Z6,P01848） T cell receptor beta variable 6-5,M1-specific T cell receptor beta chain,T cell receptor beta constant 2 × 1 （A0A0G2JMB4,A0A0K0K1A5,P0DSE2） CHOLEST-5-EN-3-YL HYDROGEN SULFATE × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CD3E_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain e； PDBConstruct 1–207； UniProt 1–207 Author chain f； PDBConstruct 1–207； UniProt 1–207

T-cell surface glycoprotein CD3 gamma chain

Homo sapiens

UniProt P09693

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 8	T-cell surface glycoprotein CD3 zeta chain × 2 （P20963） T-cell surface glycoprotein CD3 delta chain × 1 （P04234） T-cell surface glycoprotein CD3 epsilon chain × 2 （P07766） T cell receptor alpha variable 12-3,Possible J 11 gene segment,T cell receptor alpha chain constant × 1 （A0A0B4J271,A0N4Z6,P01848） T cell receptor beta variable 6-5,M1-specific T cell receptor beta chain,T cell receptor beta constant 2 × 1 （A0A0G2JMB4,A0A0K0K1A5,P0DSE2） CHOLEST-5-EN-3-YL HYDROGEN SULFATE × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CD3G_HUMAN
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain g； PDBConstruct 1–182； UniProt 1–182

T cell receptor alpha variable 12-3,Possible J 11 gene segment,T cell receptor alpha chain constant

Homo sapiens

UniProt A0A0B4J271

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 8	T-cell surface glycoprotein CD3 zeta chain × 2 （P20963） T-cell surface glycoprotein CD3 delta chain × 1 （P04234） T-cell surface glycoprotein CD3 epsilon chain × 2 （P07766） T-cell surface glycoprotein CD3 gamma chain × 1 （P09693） T cell receptor beta variable 6-5,M1-specific T cell receptor beta chain,T cell receptor beta constant 2 × 1 （A0A0G2JMB4,A0A0K0K1A5,P0DSE2） CHOLEST-5-EN-3-YL HYDROGEN SULFATE × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TVAL3_HUMAN
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain m； PDBConstruct 1–113； UniProt 2–114

T cell receptor alpha variable 12-3,Possible J 11 gene segment,T cell receptor alpha chain constant

Homo sapiens

UniProt A0N4Z6

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 8	T-cell surface glycoprotein CD3 zeta chain × 2 （P20963） T-cell surface glycoprotein CD3 delta chain × 1 （P04234） T-cell surface glycoprotein CD3 epsilon chain × 2 （P07766） T-cell surface glycoprotein CD3 gamma chain × 1 （P09693） T cell receptor beta variable 6-5,M1-specific T cell receptor beta chain,T cell receptor beta constant 2 × 1 （A0A0G2JMB4,A0A0K0K1A5,P0DSE2） CHOLEST-5-EN-3-YL HYDROGEN SULFATE × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0N4Z6_HUMAN
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain m； PDBConstruct 115–131； UniProt 4–20

T cell receptor alpha variable 12-3,Possible J 11 gene segment,T cell receptor alpha chain constant

Homo sapiens

UniProt P01848

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 8	T-cell surface glycoprotein CD3 zeta chain × 2 （P20963） T-cell surface glycoprotein CD3 delta chain × 1 （P04234） T-cell surface glycoprotein CD3 epsilon chain × 2 （P07766） T-cell surface glycoprotein CD3 gamma chain × 1 （P09693） T cell receptor beta variable 6-5,M1-specific T cell receptor beta chain,T cell receptor beta constant 2 × 1 （A0A0G2JMB4,A0A0K0K1A5,P0DSE2） CHOLEST-5-EN-3-YL HYDROGEN SULFATE × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TRAC_HUMAN
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain m； PDBConstruct 133–272； UniProt 1–140

T cell receptor beta variable 6-5,M1-specific T cell receptor beta chain,T cell receptor beta constant 2

Homo sapiens

UniProt A0A0G2JMB4

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 8	T-cell surface glycoprotein CD3 zeta chain × 2 （P20963） T-cell surface glycoprotein CD3 delta chain × 1 （P04234） T-cell surface glycoprotein CD3 epsilon chain × 2 （P07766） T-cell surface glycoprotein CD3 gamma chain × 1 （P09693） T cell receptor alpha variable 12-3,Possible J 11 gene segment,T cell receptor alpha chain constant × 1 （A0A0B4J271,A0N4Z6,P01848） CHOLEST-5-EN-3-YL HYDROGEN SULFATE × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A0G2JMB4_HUMAN
Isoform	—
PDB entities	6
Chains and sequence ranges	Author chain n； PDBConstruct 143–312； UniProt 10–179

T cell receptor beta variable 6-5,M1-specific T cell receptor beta chain,T cell receptor beta constant 2

Homo sapiens

UniProt A0A0K0K1A5

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 8	T-cell surface glycoprotein CD3 zeta chain × 2 （P20963） T-cell surface glycoprotein CD3 delta chain × 1 （P04234） T-cell surface glycoprotein CD3 epsilon chain × 2 （P07766） T-cell surface glycoprotein CD3 gamma chain × 1 （P09693） T cell receptor alpha variable 12-3,Possible J 11 gene segment,T cell receptor alpha chain constant × 1 （A0A0B4J271,A0N4Z6,P01848） CHOLEST-5-EN-3-YL HYDROGEN SULFATE × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TVB65_HUMAN
Isoform	—
PDB entities	6
Chains and sequence ranges	Author chain n； PDBConstruct 1–112； UniProt 1–112

T cell receptor beta variable 6-5,M1-specific T cell receptor beta chain,T cell receptor beta constant 2

Homo sapiens

UniProt P0DSE2

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 8	T-cell surface glycoprotein CD3 zeta chain × 2 （P20963） T-cell surface glycoprotein CD3 delta chain × 1 （P04234） T-cell surface glycoprotein CD3 epsilon chain × 2 （P07766） T-cell surface glycoprotein CD3 gamma chain × 1 （P09693） T cell receptor alpha variable 12-3,Possible J 11 gene segment,T cell receptor alpha chain constant × 1 （A0A0B4J271,A0N4Z6,P01848） CHOLEST-5-EN-3-YL HYDROGEN SULFATE × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TRBR1_HUMAN
Isoform	—
PDB entities	6
Chains and sequence ranges	Author chain n； PDBConstruct 121–142； UniProt 119–140

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	7fjf
Deposition date deposition_date	2021-08-03
Structure title title	Cryo-EM structure of a membrane protein(CS)
Keywords keywords	membrane, immune, IMMUNE SYSTEM; IMMUNE SYSTEM
Experimental Method method	ELECTRON MICROSCOPY

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

7fjf__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

7fjf__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7fjf__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	37.18 Å
Rg (electron density)	37.67 Å
Total Rg	37.96 Å
Atom count	8377
Residues	1058
Excluded volume	149870 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7fjf__assembly_1__model_1`	octameric （8）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Description description	T-cell surface glycoprotein CD3 zeta chain
Molecular weight formula_weight	18810.5 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	b,a
Atom count atom_count	8377

MKWKALFTAAILQAQLPITEAQSFGLLDPKLCYLLDGILFIYGVILTALFLRVKFSRSADAPAYQQGQNQLYNELNLGRREEYDVLDKRRGRDPEMGGKPQRRKNPQEGLYNELQKDKMAEAYSEIGMKGERRRGKGHDGLYQGLSTATKDTYDALHMQALPPRS

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Homo sapiens

Entity 2 Entity 2 polymer

Description description	T-cell surface glycoprotein CD3 delta chain
Molecular weight formula_weight	18949.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	d

MEHSTFLSGLVLATLLSQVSPFKIPIEELEDRVFVNCNTSITWVEGTVGTLLSDITRLDLGKRILDPRGIYRCNGTDIYKDKESTVQVHYRMCQSCVELDPATVAGIIVTDVIATLLLALGVFCFAGHETGRLSGAADTQALLRNDQVYQPLRDRDDAQYSHLGGNWARNK

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Homo sapiens

Entity 3 Entity 3 polymer

Description description	T-cell surface glycoprotein CD3 epsilon chain
Molecular weight formula_weight	23174.2 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	e,f

MQSGTHWRVLGLCLLSVGVWGQDGNEEMGGITQTPYKVSISGTTVILTCPQYPGSEILWQHNDKNIGGDEDDKNIGSDEDHLSLKEFSELEQSGYYVCYPRGSKPEDANFYLYLRARVCENCMEMDVMSVATIVIVDICITGGLLLLVYYWSKNRKAKAKPVTRGAGAGGRQRGQNKERPPPVPNPDYEPIRKGQRDLYSGLNQRRI

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Homo sapiens

Entity 4 Entity 4 polymer

Description description	T-cell surface glycoprotein CD3 gamma chain
Molecular weight formula_weight	20493.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	g

MEQGKGLAVLILAIILLQGTLAQSIKGNHLVKVYDYQEDGSVLLTCDAEAKNITWFKDGKMIGFLTEDKKKWNLGSNAKDPRGMYQCKGSQNKSKPLQVYYRMCQNCIELNAATISGFLFAEIVSIFVLAVGVYFIAGQDGVRQSRASDKQTLLPNDQLYQPLKDREDDQYSHLQGNQLRRN

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Homo sapiens

Entity 5 Entity 5 polymer

Description description	T cell receptor alpha variable 12-3,Possible J 11 gene segment,T cell receptor alpha chain constant
Molecular weight formula_weight	30763.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	m

MKSLRVLLVILWLQLSWVWSQQKEVEQDPGPLSVPEGAIVSLNCTYSNSAFQYFMWYRQYSRKGPELLMYTYSSGNKEDGRFTAQVDKSSKYISLFIRDSQPSDSATYLCAMSKGYSTLTFGKGTMLLVSPDIQNPDPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKTVLDMRSMDFKSNSAVAWSNKSDFACANAFNNSIIPEDTFFPSPESSCDVKLVEKSFETDTNLNFQNLSVIGFRILLLKVAGFNLLMTLRLWSS

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Homo sapiens

Entity 6 Entity 6 polymer

Description description	T cell receptor beta variable 6-5,M1-specific T cell receptor beta chain,T cell receptor beta constant 2
Molecular weight formula_weight	34614.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	n

MSISLLCCAALSLLWAGPVNAGVTQTPKFQVLKTGQSMTLQCAQDMNHEYMSWYRQDPGMGLRLIHYSVGAGITDQGEVPNGYNVSRSTTEDFPLRLLSAAPSQTSVYFCASRRRQGASGEQYFGPGTRLTVTEDLKNVFPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVSTDPQPLKEQPALNDSRYCLSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGRADCGFTSESYQQGVLSATILYEILLGKATLYAVLVSALVLMAMVKRKDSRG

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Homo sapiens

Entity 7 Entity 7 non-polymer

Description description	CHOLEST-5-EN-3-YL HYDROGEN SULFATE
Molecular weight formula_weight	466.7 kDa
Source method src_method	syn
Copy count entity_count	2

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	—

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	3.10 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	1028575

Cryo-EM structure of a membrane protein(CS)

1. Protein Identity and Related Structures Protein Identity & Related Structures

T-cell surface glycoprotein CD3 zeta chain

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

T-cell surface glycoprotein CD3 delta chain

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

T-cell surface glycoprotein CD3 epsilon chain

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

T-cell surface glycoprotein CD3 gamma chain

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

T cell receptor alpha variable 12-3,Possible J 11 gene segment,T cell receptor alpha chain constant

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

T cell receptor alpha variable 12-3,Possible J 11 gene segment,T cell receptor alpha chain constant

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

T cell receptor alpha variable 12-3,Possible J 11 gene segment,T cell receptor alpha chain constant

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

T cell receptor beta variable 6-5,M1-specific T cell receptor beta chain,T cell receptor beta constant 2

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

T cell receptor beta variable 6-5,M1-specific T cell receptor beta chain,T cell receptor beta constant 2

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

T cell receptor beta variable 6-5,M1-specific T cell receptor beta chain,T cell receptor beta constant 2

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer