9jy2

Fab-CD3-delta epsilon-TCR complex

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	Protein heterocomplex	Heteromer	Protein 10	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 delta constant × 1 （B7Z8K6） T cell receptor gamma constant 1 × 1 （P0CF51） Fab light chain × 1 Fab heavy chain × 1 CHOLESTEROL × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 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 1–31； UniProt 26–56 Author chain b； PDBConstruct 1–31； UniProt 26–56

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	Protein heterocomplex	Heteromer	Protein 10	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 delta constant × 1 （B7Z8K6） T cell receptor gamma constant 1 × 1 （P0CF51） Fab light chain × 1 Fab heavy chain × 1 CHOLESTEROL × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 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 1–105； UniProt 22–126

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	Protein heterocomplex	Heteromer	Protein 10	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 delta constant × 1 （B7Z8K6） T cell receptor gamma constant 1 × 1 （P0CF51） Fab light chain × 1 Fab heavy chain × 1 CHOLESTEROL × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 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 1–122； UniProt 33–154 Author chain f； PDBConstruct 1–122； UniProt 33–154

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	Protein heterocomplex	Heteromer	Protein 10	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 delta constant × 1 （B7Z8K6） T cell receptor gamma constant 1 × 1 （P0CF51） Fab light chain × 1 Fab heavy chain × 1 CHOLESTEROL × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 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 1–115； UniProt 26–140

T cell receptor delta constant

Homo sapiens

UniProt B7Z8K6

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 10	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 gamma constant 1 × 1 （P0CF51） Fab light chain × 1 Fab heavy chain × 1 CHOLESTEROL × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TRDC_HUMAN
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain m； PDBConstruct 1–36； UniProt 117–152

T cell receptor gamma constant 1

Homo sapiens

UniProt P0CF51

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 10	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 delta constant × 1 （B7Z8K6） Fab light chain × 1 Fab heavy chain × 1 CHOLESTEROL × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TRGC1_HUMAN
Isoform	—
PDB entities	6
Chains and sequence ranges	Author chain n； PDBConstruct 1–38； UniProt 127–164

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	9jy2
Deposition date deposition_date	2024-10-12
Structure title title	Fab-CD3-delta epsilon-TCR complex
Keywords keywords	T cell receptor, gamma delta TCR, immune cell, Fab complex, 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.

9jy2__assembly_1__model_1

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

Download this curve (.dat)

9jy2__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9jy2__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	37.63 Å
Rg (electron density)	38.28 Å
Total Rg	38.34 Å
Atom count	6515
Residues	818
Excluded volume	117520 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9jy2__assembly_1__model_1`	decameric （10）	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 (10)

Entity 1 Entity 1 polymer

Description description	T-cell surface glycoprotein CD3 zeta chain
Molecular weight formula_weight	3561.4 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	a,b
Atom count atom_count	6515

LLDPKLCYLLDGILFIYGVILTALFLRVKFS

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	11693.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	d

FKIPIEELEDRVFVNCNTSITWVEGTVGTLLSDITRLDLGKRILDPRGIYRCNGTDIYKDKESTVQVHYRMCQSCVELDPATVAGIIVTDVIATLLLALGVFCFA

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	13825.6 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

QTPYKVSISGTTVILTCPQYPGSEILWQHNDKNIGGDEDDKNIGSDEDHLSLKEFSELEQSGYYVCYPRGSKPEDANFYLYLRARVCENCMEMDVMSVATIVIVDICITGGLLLLVYYWSKN

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	12943.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	g

KGNHLVKVYDYQEDGSVLLTCDAEAKNITWFKDGKMIGFLTEDKKKWNLGSNAKDPRGMYQCKGSQNKSKPLQVYYRMCQNCIELNAATISGFLFAEIVSIFVLAVGVYFIAGQD

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 delta constant
Molecular weight formula_weight	4090.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	m

VHTEKVNMMSLTVLGLRMLFAKTVAVNFLLTAKLFF

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 gamma constant 1
Molecular weight formula_weight	4447.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	n

DTLLLQLTNTSAYYMYLLLLLKSVVYFAIITCCLLRRT

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 polymer

Description description	Fab light chain
Molecular weight formula_weight	11491.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A

DIQMTQTTSSLSASLGDRVTISCRASQDIRNYLNWYQQKPDGTVKLLIYYTSRLHSGVPSKFSGSGSGTDYSLTISNLEQEDIATYFCQQGNTLPWTFAGGTKL

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 8 Entity 8 polymer

Description description	Fab heavy chain
Molecular weight formula_weight	13563.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

EVQLQQSGPELVKPGASMKISCKASGYSFTGYTMNWVKQSHGKNLEWMGLINPYKGVSTYNQKFKDKATLTVDKSSSTAYMELLSLTSEDSAVYYCARSGYYGDSDWYFDVWGQGTTLTVF

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 9 Entity 9 non-polymer

Description description	CHOLESTEROL
Molecular weight formula_weight	386.7 kDa
Source method src_method	syn
Copy count entity_count	1

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	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	3.240 Å
Low-resolution limit resolution_low	— Å
R factor r_factor	—
R_work r_work	—
R_free r_free	—

Resolution resolution	3.24 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	232138

Fab-CD3-delta epsilon-TCR complex

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 delta 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 gamma constant 1

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

9jy2__assembly_1__model_1

9jy2__assembly_1__model_1 | I(q)

9jy2__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

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

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 polymer

Polymer Polymer

Source Source

Entity 6 Entity 6 polymer

Polymer Polymer

Source Source

Entity 7 Entity 7 polymer