7phr

Structure of a fully assembled T-cell receptor engaging a tumor-associated peptide-MHC I

Method: ELECTRON MICROSCOPY

▼

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

T-cell surface glycoprotein CD3 gamma chain

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 11	T-cell receptor alpha chain × 1 T-cell receptor beta chain × 1 T-cell surface glycoprotein CD3 delta chain, green fluorescent protein × 1 （P04234,P42212） T-cell surface glycoprotein CD3 epsilon chain × 2 （P07766） HLA class I histocompatibility antigen, A alpha chain × 1 （P04439） Beta-2-microglobulin × 1 （P61769） Tumor-associated antigentic peptide gp100 × 1 （P40967） T-cell surface glycoprotein CD3 zeta chain × 2 （P20963） 2-acetamido-2-deoxy-beta-D-glucopyranose × 6	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	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–122； UniProt 23–144

T-cell surface glycoprotein CD3 delta chain, green fluorescent protein

Aequorea victoria

UniProt P04234

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 11	T-cell receptor alpha chain × 1 T-cell receptor beta chain × 1 T-cell surface glycoprotein CD3 gamma chain × 1 （P09693） T-cell surface glycoprotein CD3 epsilon chain × 2 （P07766） HLA class I histocompatibility antigen, A alpha chain × 1 （P04439） Beta-2-microglobulin × 1 （P61769） Tumor-associated antigentic peptide gp100 × 1 （P40967） T-cell surface glycoprotein CD3 zeta chain × 2 （P20963） 2-acetamido-2-deoxy-beta-D-glucopyranose × 6	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	4
Chains and sequence ranges	Author chain D； PDBConstruct 1–111； UniProt 22–132

T-cell surface glycoprotein CD3 delta chain, green fluorescent protein

Aequorea victoria

UniProt P42212

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 11	T-cell receptor alpha chain × 1 T-cell receptor beta chain × 1 T-cell surface glycoprotein CD3 gamma chain × 1 （P09693） T-cell surface glycoprotein CD3 epsilon chain × 2 （P07766） HLA class I histocompatibility antigen, A alpha chain × 1 （P04439） Beta-2-microglobulin × 1 （P61769） Tumor-associated antigentic peptide gp100 × 1 （P40967） T-cell surface glycoprotein CD3 zeta chain × 2 （P20963） 2-acetamido-2-deoxy-beta-D-glucopyranose × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	GFP_AEQVI
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain D； PDBConstruct 118–356； UniProt 1–238

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 11	T-cell receptor alpha chain × 1 T-cell receptor beta chain × 1 T-cell surface glycoprotein CD3 gamma chain × 1 （P09693） T-cell surface glycoprotein CD3 delta chain, green fluorescent protein × 1 （P04234,P42212） HLA class I histocompatibility antigen, A alpha chain × 1 （P04439） Beta-2-microglobulin × 1 （P61769） Tumor-associated antigentic peptide gp100 × 1 （P40967） T-cell surface glycoprotein CD3 zeta chain × 2 （P20963） 2-acetamido-2-deoxy-beta-D-glucopyranose × 6	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	5
Chains and sequence ranges	Author chain E； PDBConstruct 1–136； UniProt 23–158 Author chain e； PDBConstruct 1–136； UniProt 23–158

HLA class I histocompatibility antigen, A alpha chain

Homo sapiens

UniProt P04439

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 11	T-cell receptor alpha chain × 1 T-cell receptor beta chain × 1 T-cell surface glycoprotein CD3 gamma chain × 1 （P09693） T-cell surface glycoprotein CD3 delta chain, green fluorescent protein × 1 （P04234,P42212） T-cell surface glycoprotein CD3 epsilon chain × 2 （P07766） Beta-2-microglobulin × 1 （P61769） Tumor-associated antigentic peptide gp100 × 1 （P40967） T-cell surface glycoprotein CD3 zeta chain × 2 （P20963） 2-acetamido-2-deoxy-beta-D-glucopyranose × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	HLAA_HUMAN
Isoform	—
PDB entities	6
Chains and sequence ranges	Author chain H； PDBConstruct 13–292； UniProt 25–304

Beta-2-microglobulin

Homo sapiens

UniProt P61769

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 11	T-cell receptor alpha chain × 1 T-cell receptor beta chain × 1 T-cell surface glycoprotein CD3 gamma chain × 1 （P09693） T-cell surface glycoprotein CD3 delta chain, green fluorescent protein × 1 （P04234,P42212） T-cell surface glycoprotein CD3 epsilon chain × 2 （P07766） HLA class I histocompatibility antigen, A alpha chain × 1 （P04439） Tumor-associated antigentic peptide gp100 × 1 （P40967） T-cell surface glycoprotein CD3 zeta chain × 2 （P20963） 2-acetamido-2-deoxy-beta-D-glucopyranose × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	B2MG_HUMAN
Isoform	—
PDB entities	7
Chains and sequence ranges	Author chain L； PDBConstruct 2–101； UniProt 20–119

Tumor-associated antigentic peptide gp100

OrganismNot specified

UniProt P40967

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 11	T-cell receptor alpha chain × 1 T-cell receptor beta chain × 1 T-cell surface glycoprotein CD3 gamma chain × 1 （P09693） T-cell surface glycoprotein CD3 delta chain, green fluorescent protein × 1 （P04234,P42212） T-cell surface glycoprotein CD3 epsilon chain × 2 （P07766） HLA class I histocompatibility antigen, A alpha chain × 1 （P04439） Beta-2-microglobulin × 1 （P61769） T-cell surface glycoprotein CD3 zeta chain × 2 （P20963） 2-acetamido-2-deoxy-beta-D-glucopyranose × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PMEL_HUMAN
Isoform	—
PDB entities	8
Chains and sequence ranges	Author chain P； PDBConstruct 1–9； UniProt 280–288

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 11	T-cell receptor alpha chain × 1 T-cell receptor beta chain × 1 T-cell surface glycoprotein CD3 gamma chain × 1 （P09693） T-cell surface glycoprotein CD3 delta chain, green fluorescent protein × 1 （P04234,P42212） T-cell surface glycoprotein CD3 epsilon chain × 2 （P07766） HLA class I histocompatibility antigen, A alpha chain × 1 （P04439） Beta-2-microglobulin × 1 （P61769） Tumor-associated antigentic peptide gp100 × 1 （P40967） 2-acetamido-2-deoxy-beta-D-glucopyranose × 6	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	9
Chains and sequence ranges	Author chain Z； PDBConstruct 1–36； UniProt 22–57 Author chain z； PDBConstruct 1–36； UniProt 22–57

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	7phr
Deposition date deposition_date	2021-08-18
Structure title title	Structure of a fully assembled T-cell receptor engaging a tumor-associated peptide-MHC I
Keywords keywords	T-cell receptor, TCR, Major Histocompatibility Complex, MHC, Antigen, Adaptive Immunity, Cancer, Complex, IMMUNE SYSTEM; IMMUNE SYSTEM
Experimental Method method	ELECTRON MICROSCOPY

▼

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.

7phr__assembly_1__model_1

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

Download this curve (.dat)

7phr__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7phr__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	46.05 Å
Rg (electron density)	47.61 Å
Total Rg	47.50 Å
Atom count	11511
Residues	1443
Excluded volume	204090 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7phr__assembly_1__model_1`	undecameric （11）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (10)

Entity 1 Entity 1 polymer

Description description	T-cell receptor alpha chain
Molecular weight formula_weight	27979.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	11511

MSQQGEEDPQALSIQEGENATMNCSYKTSINNLQWYRQNSGRGLVHLILIRSNEREKHSGRLRVTLDTSKKSSSLLITASRAADTASYFCATDGSTPMQFGKGTRLSVIPNIQNPDPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKTVLDMRSMDFKSNSAVAWSNKSDFACANAFNNSIIPEDTFFPSPESSCDVKLVEKSFETDTNLNFQNLSVIGFRILLLKVAGFNLLMTLRLWSS

Source Source

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

Entity 2 Entity 2 polymer

Description description	T-cell receptor beta chain
Molecular weight formula_weight	32750.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MDGGITQSPKYLFRKEGQNVTLSCEQNLNHDAMYWYRQDPGQGLRLIYYSWAQGDFQKGDIAEGYSVSREKKESFPLTVTSAQKNPTAFYLCASSWGAPYEQYFGPGTRLTVTEDLNKVFPPEVAVFEPSEAEISHTQKATLVCLATGFFPDHVELSWWVNGKEVHSGVSTDPQPLKEQPALNDSRYCLSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGRADCGFTSVSYQQGVLSATILYEILLGKATLYAVLVSALVLMAMVKRKDF

Source Source

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

Entity 3 Entity 3 polymer

Description description	T-cell surface glycoprotein CD3 gamma chain
Molecular weight formula_weight	13713.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

QSIKGNHLVKVYDYQEDGSVLLTCDAEAKNITWFKDGKMIGFLTEDKKKWNLGSNAKDPRGMYQCKGSQNKSKPLQVYYRMCQNCIELNAATISGFLFAEIVSIFVLAVGVYFIAGQDGVRQ

Source Source

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

Entity 4 Entity 4 polymer

Description description	T-cell surface glycoprotein CD3 delta chain, green fluorescent protein
Molecular weight formula_weight	39858.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

FKIPIEELEDRVFVNCNTSITWVEGTVGTLLSDITRLDLGKRILDPRGIYRCNGTDIYKDKESTVQVHYRMCQSCVELDPATVAGIIVTDVIATLLLALGVFCFAGHETGRDPPVATMVSKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTLSYGVQCFSRYPDHMKQHDFFKSAMPEGYVQERTIFFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIKVNFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSALSKDPNEKRDHMVLLEFVTAAGITLGMDELYK

Source Source

Source organism organism	Aequorea victoria
Common name common_name	Water jellyfish, Mesonema victoria
NCBI taxonomy ID ncbi_taxonomy_id	6100
Host organism host_organism	Cricetulus griseus

Entity 5 Entity 5 polymer

Description description	T-cell surface glycoprotein CD3 epsilon chain
Molecular weight formula_weight	15316.2 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

DGNEEMGGITQTPYKVSISGTTVILTCPQYPGSEILWQHNDKNIGGDEDDKNIGSDEDHLSLKEFSELEQSGYYVCYPRGSKPEDANFYLYLRARVCENCMEMDVMSVATIVIVDICITGGLLLLVYYWSKNRKAK

Source Source

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

Entity 6 Entity 6 polymer

Description description	HLA class I histocompatibility antigen, A alpha chain
Molecular weight formula_weight	35054.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H

MGSSHHHHHHGSGSHSMRYFFTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEYWDGETRKVKAHSQTHRVDLGTLRGYYNQSEAGSHTVQRMYGCDVGSDWRFLRGYHQYAYDGKDYIALKEDLRSWTAADMAAQTTKHKWEAAHVAEQLRAYLEGTCVEWLRRYLENGKETLQRTDAPKTHMTHHAVSDHEATLRCWALSFYPAEITLTWQRDGEDQTQDTELVETRPAGDGTFQKWAAVVVPSGQEQRYTCHVQHEGLPKPLTLRWEPSSQPEDQVDPRLIDGK

Source Source

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

Entity 7 Entity 7 polymer

Description description	Beta-2-microglobulin
Molecular weight formula_weight	11936.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L

MGIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKDWSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Source Source

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

Entity 8 Entity 8 polymer

Description description	Tumor-associated antigentic peptide gp100
Molecular weight formula_weight	974.1 kDa
Mutation mutation	A9V
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	P

YLEPGPVTV

Entity 9 Entity 9 polymer

Description description	T-cell surface glycoprotein CD3 zeta chain
Molecular weight formula_weight	4138.0 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	Z,z

QSFGLLDPKLCYLLDGILFIYGVILTALFLRVKFSR

Source Source

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

Entity 10 Entity 10 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	syn
Copy count entity_count	6

▼

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	7phrH01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	500 — Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — MHC class I-like antigen recognition-like

Domain ID domain_id	7phrH02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

▶

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	3.08 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	154408

Structure of a fully assembled T-cell receptor engaging a tumor-associated peptide-MHC I

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

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 surface glycoprotein CD3 delta chain, green fluorescent protein

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, green fluorescent protein

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

HLA class I histocompatibility antigen, A alpha 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

Beta-2-microglobulin

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Tumor-associated antigentic peptide gp100

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 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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

7phr__assembly_1__model_1

7phr__assembly_1__model_1 | I(q)

7phr__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (10)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer