9jy3

delta epsilon/gamma epsilon Fab-TCR tetramer

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 20	T-cell surface glycoprotein CD3 delta chain × 2 （P04234） T-cell surface glycoprotein CD3 epsilon chain × 4 （P07766） T-cell surface glycoprotein CD3 gamma chain × 2 （P09693） T cell receptor delta constant × 2 （B7Z8K6） T cell receptor gamma constant 1 × 2 （P0CF51） Fab light chain × 2 Fab heavy chain × 2 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 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 20	T-cell surface glycoprotein CD3 zeta chain × 4 （P20963） T-cell surface glycoprotein CD3 epsilon chain × 4 （P07766） T-cell surface glycoprotein CD3 gamma chain × 2 （P09693） T cell receptor delta constant × 2 （B7Z8K6） T cell receptor gamma constant 1 × 2 （P0CF51） Fab light chain × 2 Fab heavy chain × 2 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 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 20	T-cell surface glycoprotein CD3 zeta chain × 4 （P20963） T-cell surface glycoprotein CD3 delta chain × 2 （P04234） T-cell surface glycoprotein CD3 gamma chain × 2 （P09693） T cell receptor delta constant × 2 （B7Z8K6） T cell receptor gamma constant 1 × 2 （P0CF51） Fab light chain × 2 Fab heavy chain × 2 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 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 20	T-cell surface glycoprotein CD3 zeta chain × 4 （P20963） T-cell surface glycoprotein CD3 delta chain × 2 （P04234） T-cell surface glycoprotein CD3 epsilon chain × 4 （P07766） T cell receptor delta constant × 2 （B7Z8K6） T cell receptor gamma constant 1 × 2 （P0CF51） Fab light chain × 2 Fab heavy chain × 2 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 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 20	T-cell surface glycoprotein CD3 zeta chain × 4 （P20963） T-cell surface glycoprotein CD3 delta chain × 2 （P04234） T-cell surface glycoprotein CD3 epsilon chain × 4 （P07766） T-cell surface glycoprotein CD3 gamma chain × 2 （P09693） T cell receptor gamma constant 1 × 2 （P0CF51） Fab light chain × 2 Fab heavy chain × 2 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 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 20	T-cell surface glycoprotein CD3 zeta chain × 4 （P20963） T-cell surface glycoprotein CD3 delta chain × 2 （P04234） T-cell surface glycoprotein CD3 epsilon chain × 4 （P07766） T-cell surface glycoprotein CD3 gamma chain × 2 （P09693） T cell receptor delta constant × 2 （B7Z8K6） Fab light chain × 2 Fab heavy chain × 2 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 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	9jy3
Deposition date deposition_date	2024-10-12
Structure title title	delta epsilon/gamma epsilon Fab-TCR tetramer
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.

9jy3__assembly_1__model_1

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

Download this curve (.dat)

9jy3__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9jy3__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	56.73 Å
Rg (electron density)	58.54 Å
Total Rg	58.48 Å
Atom count	15638
Residues	1998
Excluded volume	281080 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9jy3__assembly_1__model_1`	eicosameric （20）	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 (9)

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	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,a,b
Atom count atom_count	15638

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	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,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	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E,F,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	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G,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	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	M,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	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	N,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	23475.9 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	O,Q

DIQMTQTTSSLSASLGDRVTISCRASQDIRNYLNWYQQKPDGTVKLLIYYTSRLHSGVPSKFSGSGSGTDYSLTISNLEQEDIATYFCQQGNTLPWTFAGGTKLEIKRADAAPTVSIFPPASEQLTSGGASVVCFLNNFYPKSINSKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKNEYERHNSYTCEATHKTSTSPIVKSFNRS

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	24003.0 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	P,R

EVQLQQSGPELVKPGASMKISCKASGYSFTGYTMNWVKQSHGKNLEWMGLINPYKGVSTYNQKFKDKATLTVDKSSSTAYMELLSLTSEDSAVYYCARSGYYGDSDWYFDVWGQGTTLTVFSAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLKSDLYTLSSSVTVPSSPRPSETVTCNVAHPASSTTVDKKIVPR

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

Resolution resolution	3.35 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	47513

delta epsilon/gamma epsilon Fab-TCR tetramer

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

9jy3__assembly_1__model_1

9jy3__assembly_1__model_1 | I(q)

9jy3__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 (9)

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