5m00

Crystal structure of murine P14 TCR complex with H-2Db and Y4A, modified gp33 peptide from LCMV

Method: X-RAY DIFFRACTION

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

H-2 class I histocompatibility antigen, D-B alpha chain

Mus musculus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 5	Beta-2-microglobulin × 1 （P01887） Protein Trav14-1,Uncharacterized protein × 1 （A0A0G2JF94,Q6PIR9） T-cell receptor beta chain V region C5,Uncharacterized protein × 1 （P04213,Q7TND8） LCMV-DERIVED GP33 ALTERED PEPTIDE LIGAND Y4A × 1 water × 5	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	HA11_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–276； UniProt 25–300

Beta-2-microglobulin

Mus musculus

UniProt P01887

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 5	H-2 class I histocompatibility antigen, D-B alpha chain × 1 （P01899） Protein Trav14-1,Uncharacterized protein × 1 （A0A0G2JF94,Q6PIR9） T-cell receptor beta chain V region C5,Uncharacterized protein × 1 （P04213,Q7TND8） LCMV-DERIVED GP33 ALTERED PEPTIDE LIGAND Y4A × 1 water × 5	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	B2MG_MOUSE
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 21–119； UniProt 21–119

Protein Trav14-1,Uncharacterized protein

Mus musculus

UniProt A0A0G2JF94

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 5	H-2 class I histocompatibility antigen, D-B alpha chain × 1 （P01899） Beta-2-microglobulin × 1 （P01887） T-cell receptor beta chain V region C5,Uncharacterized protein × 1 （P04213,Q7TND8） LCMV-DERIVED GP33 ALTERED PEPTIDE LIGAND Y4A × 1 water × 5	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A0G2JF94_MOUSE
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain G； PDBConstruct 1–99； UniProt 22–120

Protein Trav14-1,Uncharacterized protein

Mus musculus

UniProt Q6PIR9

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 5	H-2 class I histocompatibility antigen, D-B alpha chain × 1 （P01899） Beta-2-microglobulin × 1 （P01887） T-cell receptor beta chain V region C5,Uncharacterized protein × 1 （P04213,Q7TND8） LCMV-DERIVED GP33 ALTERED PEPTIDE LIGAND Y4A × 1 water × 5	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q6PIR9_MOUSE
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain G； PDBConstruct 120–205； UniProt 135–220

T-cell receptor beta chain V region C5,Uncharacterized protein

Mus musculus

UniProt P04213

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 5	H-2 class I histocompatibility antigen, D-B alpha chain × 1 （P01899） Beta-2-microglobulin × 1 （P01887） Protein Trav14-1,Uncharacterized protein × 1 （A0A0G2JF94,Q6PIR9） LCMV-DERIVED GP33 ALTERED PEPTIDE LIGAND Y4A × 1 water × 5	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TVB5_MOUSE
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain H； PDBConstruct 1–92； UniProt 11–102

T-cell receptor beta chain V region C5,Uncharacterized protein

Mus musculus

UniProt Q7TND8

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 5	H-2 class I histocompatibility antigen, D-B alpha chain × 1 （P01899） Beta-2-microglobulin × 1 （P01887） Protein Trav14-1,Uncharacterized protein × 1 （A0A0G2JF94,Q6PIR9） LCMV-DERIVED GP33 ALTERED PEPTIDE LIGAND Y4A × 1 water × 5	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q7TND8_MOUSE
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain H； PDBConstruct 110–238； UniProt 129–257

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	5m00
Deposition date deposition_date	2016-10-03
Structure title title	Crystal structure of murine P14 TCR complex with H-2Db and Y4A, modified gp33 peptide from LCMV
Keywords keywords	MHC class I, TCR, H-2Db, gp33, LCMV, 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.

5m00__assembly_1__model_1

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

Download this curve (.dat)

5m00__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5m00__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	37.53 Å
Rg (electron density)	38.13 Å
Total Rg	38.29 Å
Atom count	6504
Residues	810
Excluded volume	114480 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5m00__assembly_1__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 (6)

Entity 1 Entity 1 polymer

Description description	H-2 class I histocompatibility antigen, D-B alpha chain
Molecular weight formula_weight	32087.7 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	6906

GPHSMRYFETAVSRPGLEEPRYISVGYVDNKEFVRFDSDAENPRYEPRAPWMEQEGPEYWERETQKAKGQEQWFRVSLRNLLGYYNQSAGGSHTLQQMSGCDLGSDWRLLRGYLQFAYEGRDYIALNEDLKTWTAADMAAQITRRKWEQSGAAEHYKAYLEGECVEWLHRYLKNGNATLLRTDSPKAHVTHHPRSKGEVTLRCWALGFYPADITLTWQLNGEELTQDMELVETRPAGDGTFQKWASVVVPLGKEQNYTCRVYHEGLPEPLTLRWEP

Source Source

Source organism organism	Mus musculus
Common name common_name	House Mouse
NCBI taxonomy ID ncbi_taxonomy_id	10090
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Beta-2-microglobulin
Molecular weight formula_weight	13795.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MARSVTLVFLVLVSLTGLMGIQKTPQIQVYSRHPPENGKPNILNCYVTQFHPPHIEIQMLKNGKKIPKVEMSDMSFSKDWSFYILAHTEFTPTETDTYACRVKHDSMAEPKTVYWDRDM

Source Source

Source organism organism	Mus musculus
Common name common_name	House Mouse
NCBI taxonomy ID ncbi_taxonomy_id	10090
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	Protein Trav14-1,Uncharacterized protein
Molecular weight formula_weight	23072.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G

QQKEKHDQQQVRQSPQSLTVWEGGTTVLTCSYEDSTFNYFPWYQQFPGEGPALLISILSVSDKKEDGRFTTFFNKREKKLSLHIIDSQPGDSATYFCAALYGNEKITFGAGTKLTIKPNIQNPEPAVYQLKDPRSQDSTLCLFTDFDSQINVPKTMESGTFITDKCVLDMKAMDSKSNGAIAWSNQTSFTCQDIFKETNATYPSS

Source Source

Source organism organism	Mus musculus
Common name common_name	House Mouse
NCBI taxonomy ID ncbi_taxonomy_id	10090
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 polymer

Description description	T-cell receptor beta chain V region C5,Uncharacterized protein
Molecular weight formula_weight	26647.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H

AVTQSPRSKVAVTGGKVTLSCHQTNNHDYMYWYRQDTGHGLRLIHYSYVADSTEKGDIPDGYKASRPSQENFSLILELASLSQTAVYFCASSDAGGRNTLYFGAGTRLSVLEDLRNVTPPKVSLFEPSKAEIANKQKATLVCLARGFFPDHVELSWWVNGKEVHSGVCTDPQAYKESNYSYSLSSRLRVSATFWHNPRNHFRCQVQFHGLSEEDKWPEGSPKPVTQNISAEAWGRADC

Source Source

Source organism organism	Mus musculus
Common name common_name	House Mouse
NCBI taxonomy ID ncbi_taxonomy_id	10090
Host organism host_organism	Escherichia coli

Entity 5 Entity 5 polymer

Description description	LCMV-DERIVED GP33 ALTERED PEPTIDE LIGAND Y4A
Molecular weight formula_weight	953.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	P

KAVANFATM

Source Source

Source organism organism	Mus musculus
Common name common_name	House Mouse
NCBI taxonomy ID ncbi_taxonomy_id	10090
Host organism host_organism	Escherichia coli

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	381

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6. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d5m00a1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.19 — MHC antigen-recognition domain
Superfamily Superfamily superfamily	d.19.1 — MHC antigen-recognition domain
Family Family family	d.19.1.1 — MHC antigen-recognition domain

Domain ID domain_id	d5m00a2
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.2 — C1 set domains (antibody constant domain-like)

Domain ID domain_id	d5m00b1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.2 — C1 set domains (antibody constant domain-like)

Domain ID domain_id	d5m00b2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d5m00g1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.0 — automated matches

Domain ID domain_id	d5m00g2
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.2 — C1 set domains (antibody constant domain-like)

Domain ID domain_id	d5m00h1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.0 — automated matches

Domain ID domain_id	d5m00h2
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.2 — C1 set domains (antibody constant domain-like)

CATH v4.4 (6 domains)

Domain ID domain_id	5m00A01
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	5m00A02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5m00B00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5m00G01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5m00H01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5m00H02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

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Unit-cell length a length_a	258.455 Å
Unit-cell length b length_b	46.941 Å
Unit-cell length c length_c	90.253 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	94.24 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	1.950 Å
Low-resolution limit resolution_low	128.870 Å
R factor r_factor	0.2015
R_work r_work	0.1996
R_free r_free	0.2371

Crystal structure of murine P14 TCR complex with H-2Db and Y4A, modified gp33 peptide from LCMV

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

H-2 class I histocompatibility antigen, D-B 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

Protein Trav14-1,Uncharacterized 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

Protein Trav14-1,Uncharacterized 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 receptor beta chain V region C5,Uncharacterized 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 receptor beta chain V region C5,Uncharacterized 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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

5m00__assembly_1__model_1

5m00__assembly_1__model_1 | I(q)

5m00__assembly_1__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 (6)

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 water

6. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (8 domains)

CATH v4.4 (6 domains)