7byd

Crystal structure of SN45 TCR in complex with lipopeptide-bound Mamu-B*05104

Method: X-RAY DIFFRACTION

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

B protein

Macaca mulatta

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	Beta-2-microglobulin × 1 （Q6V7J5） GLY-GLY-ALA-ILE × 1 SN45 T cell receptor alpha chain × 1 SN45 T cell receptor beta chain × 1 IODIDE ION × 9 1,2-ETHANEDIOL × 1 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 CALCIUM ION × 1 MYRISTIC ACID × 1 water × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 5	Beta-2-microglobulin × 1 （Q6V7J5） GLY-GLY-ALA-ILE × 1 SN45 T cell receptor alpha chain × 1 SN45 T cell receptor beta chain × 1 IODIDE ION × 10 1,2-ETHANEDIOL × 3 MYRISTIC ACID × 1 SODIUM ION × 1 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	B2ZHY7_MACMU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–276； UniProt 22–297 Author chain F； PDBConstruct 1–276； UniProt 22–297

Beta-2-microglobulin

Macaca mulatta

UniProt Q6V7J5

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	B protein × 1 （B2ZHY7） GLY-GLY-ALA-ILE × 1 SN45 T cell receptor alpha chain × 1 SN45 T cell receptor beta chain × 1 IODIDE ION × 9 1,2-ETHANEDIOL × 1 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 CALCIUM ION × 1 MYRISTIC ACID × 1 water × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 5	B protein × 1 （B2ZHY7） GLY-GLY-ALA-ILE × 1 SN45 T cell receptor alpha chain × 1 SN45 T cell receptor beta chain × 1 IODIDE ION × 10 1,2-ETHANEDIOL × 3 MYRISTIC ACID × 1 SODIUM ION × 1 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	B2MG_MACMU
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–100； UniProt 20–119 Author chain G； PDBConstruct 1–100； UniProt 20–119

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	7byd
Deposition date deposition_date	2020-04-22
Structure title title	Crystal structure of SN45 TCR in complex with lipopeptide-bound Mamu-B*05104
Keywords keywords	Major histocompatibility complex class 1, T cell receptor, lipopeptide, IMMUNE SYSTEM; IMMUNE SYSTEM
Experimental Method method	X-RAY DIFFRACTION

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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.

7byd__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

7byd__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7byd__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	37.47 Å
Rg (electron density)	37.69 Å
Total Rg	37.73 Å
Atom count	6653
Residues	823
Excluded volume	117110 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7byd__assembly_1__model_1`	pentameric （5）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`7byd__assembly_2__model_1`	pentameric （5）	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 (12)

Entity 1 Entity 1 polymer

Description description	B protein
Molecular weight formula_weight	31919.2 kDa
Mutation mutation	R149E,K198E,D244E
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,F
Atom count atom_count	13311

GSHSLRYFGTAVSRPGRGEPRFIYVGYVDDTQFVRFDSDAASPRTEPRAPWVEQEGPEYWEEETRRAKARAQTDRADLRTLRGYYNQSEAGSHTLQWMAGCDLGPNGRLLRGYHQSAYDGKDYIALNEDLRSWIAADMAAQNTQRKWEATRYAERFRAYLEGPCLEWLRRYLENGKETLQHADPPKTHVTHHPVSDHEATLRCWALGFYPAEITLTWQRDGEEQTQDIEFVETRPAGDGTFQKWGAVVVPSGEEQRYTCHVQHKGLPEPLTLRWEP

Source Source

Source organism organism	Macaca mulatta
Common name common_name	Rhesus macaque
NCBI taxonomy ID ncbi_taxonomy_id	9544
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Beta-2-microglobulin
Molecular weight formula_weight	11731.2 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

AIQRTPKIQVYSRHPPENGKPNFLNCYVSGFHPSDIEVDLLKNGEKMGKVEHSDLSFSKDWSFYLLYYTEFTPNEKDEYACRVNHVTLSGPRTVKWDRDM

Source Source

Source organism organism	Macaca mulatta
Common name common_name	Rhesus macaque
NCBI taxonomy ID ncbi_taxonomy_id	9544
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	GLY-GLY-ALA-ILE
Molecular weight formula_weight	316.4 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,H

GGAI

Entity 4 Entity 4 polymer

Description description	SN45 T cell receptor alpha chain
Molecular weight formula_weight	21809.4 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

AKTTQPISMDSYEGQEVNITCNHNDIATSDYIMWYQQFPNQGPRFIIQGYKANIANEVASLFIPTDRKSSTLSLPRVALSDTAVYYCLVGGGGYVLTFGRGTSLIVHPYIQNPDPAVYQLRGSKSNDTSVCLFTDFDSVMNVSQSKDSDVHITDKCVLDMRSMDFKSNGAVAWSNKSDFACTSAFKDSVIPADTFFPG

Source Source

Source organism organism	Macaca mulatta
NCBI taxonomy ID ncbi_taxonomy_id	9544
Host organism host_organism	Escherichia coli

Entity 5 Entity 5 polymer

Description description	SN45 T cell receptor beta chain
Molecular weight formula_weight	28086.6 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

DTAVSQTPKYLVRQTGKNESLKCEQNLGHNAMYWYKQDSKKLLKIMFIYNNKEPILNETVPYRFSPKSPDKAHLNLHIKSLELGDSAVYFCASSQDLGAGEVYEQYFGPGTRLTVIEDLKKVFPPKVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQPALEDSRYCLSSRLRVSATFWHNPRNHFRCQVQFYGLSEDDEWTEDRDKPITQKISAEAWGRA

Source Source

Source organism organism	Macaca mulatta
NCBI taxonomy ID ncbi_taxonomy_id	9544
Host organism host_organism	Escherichia coli

Entity 6 Entity 6 non-polymer

Description description	IODIDE ION
Molecular weight formula_weight	126.9 kDa
Source method src_method	syn
Copy count entity_count	19

Entity 7 Entity 7 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 8 Entity 8 non-polymer

Description description	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Molecular weight formula_weight	122.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 9 Entity 9 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 10 Entity 10 non-polymer

Description description	MYRISTIC ACID
Molecular weight formula_weight	228.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 11 Entity 11 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 12 Entity 12 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	50

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Unit-cell length a length_a	83.937 Å
Unit-cell length b length_b	95.071 Å
Unit-cell length c length_c	123.352 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.89 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	monoclinic

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	41.963 Å
R factor r_factor	0.1884
R_work r_work	0.1852
R_free r_free	0.2496

Crystal structure of SN45 TCR in complex with lipopeptide-bound Mamu-B*05104

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

B 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

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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

7byd__assembly_2__model_1

7byd__assembly_2__model_1 | I(q)

7byd__assembly_2__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (12)

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

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 polymer

Polymer Polymer

Source Source

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 non-polymer

Entity 10 Entity 10 non-polymer

Entity 11 Entity 11 non-polymer

Entity 12 Entity 12 water

7. Citations (1)