SAXSdb — 7n5q

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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	Protein heterocomplex	Heteromer	Protein 3	Beta-2-microglobulin × 1 （P61769） peptide from Polymerase acidic protein × 1 （O89752） SODIUM ION × 8 ACETATE ION × 2 water × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	Beta-2-microglobulin × 1 （P61769） peptide from Polymerase acidic protein × 1 （O89752） SODIUM ION × 3 ACETATE ION × 1 water × 3	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 2–281； UniProt 25–305 Author chain F； PDBConstruct 2–281； UniProt 25–305

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	Protein heterocomplex	Heteromer	Protein 3	H-2 class I histocompatibility antigen, D-B alpha chain × 1 （P01899） peptide from Polymerase acidic protein × 1 （O89752） SODIUM ION × 8 ACETATE ION × 2 water × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	H-2 class I histocompatibility antigen, D-B alpha chain × 1 （P01899） peptide from Polymerase acidic protein × 1 （O89752） SODIUM ION × 3 ACETATE ION × 1 water × 3	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	2
Chains and sequence ranges	Author chain B； PDBConstruct 2–100； UniProt 21–119 Author chain G； PDBConstruct 2–100； UniProt 21–119

peptide from Polymerase acidic protein

OrganismNot specified

UniProt O89752

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	H-2 class I histocompatibility antigen, D-B alpha chain × 1 （P01899） Beta-2-microglobulin × 1 （P61769） SODIUM ION × 8 ACETATE ION × 2 water × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	H-2 class I histocompatibility antigen, D-B alpha chain × 1 （P01899） Beta-2-microglobulin × 1 （P61769） SODIUM ION × 3 ACETATE ION × 1 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PA_I97A1
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–10； UniProt 224–233 Author chain H； PDBConstruct 1–10； UniProt 224–233

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	7n5q
Deposition date deposition_date	2021-06-06
Structure title title	Peptide-MHC complex of mouse H2-Db presenting PA224 with E4C mutation
Keywords keywords	;Major Histocompatibility complex, MHC, mouse, Influenza A, polymerase acidic protein, H2Db, PA224-233, Cysteine, mutant, 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.

7n5q__assembly_1__model_1

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

Download this curve (.dat)

7n5q__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7n5q__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	24.64 Å
Rg (electron density)	23.65 Å
Total Rg	24.55 Å
Atom count	3223
Residues	389
Excluded volume	56780 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7n5q__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`7n5q__assembly_2__model_1`	trimeric （3）	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	32619.3 kDa
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	7029

MGPHSMRYFETAVSRPGLEEPRYISVGYVDNKEFVRFDSDAENPRYEPRAPWMEQEGPEYWERETQKAKGQEQWFRVSLRNLLGYYNQSAGGSHTLQQMSGCDLGSDWRLLRGYLQFAYEGRDYIALNEDLKTWTAADMAAQITRRKWEQSGAAEHYKAYLEGECVEWLHRYLKNGNATLLRTDSPKAHVTHHPRSKGEVTLRCWALGFYPADITLTWQLNGEELTQDMELVETRPAGDGTFQKWASVVVPLGKEQNYTCRVYHEGLPEPLTLRWEPPSTD

Source Source

Source organism organism	Mus musculus
Common name common_name	Mouse
NCBI taxonomy ID ncbi_taxonomy_id	10090
Host organism host_organism	;Escherichia coli 'BL21-Gold(DE3)pLysS AG' ;

Entity 2 Entity 2 polymer

Description description	Beta-2-microglobulin
Molecular weight formula_weight	11879.4 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKDWSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

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 'BL21-Gold(DE3)pLysS AG' ;

Entity 3 Entity 3 polymer

Description description	peptide from Polymerase acidic protein
Molecular weight formula_weight	1160.3 kDa
Mutation mutation	E4C
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

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

SSLCNFRAYV

Entity 4 Entity 4 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	nat
Copy count entity_count	11

Entity 5 Entity 5 non-polymer

Description description	ACETATE ION
Molecular weight formula_weight	59.0 kDa
Source method src_method	nat
Copy count entity_count	3

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	473

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	7n5qA01
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	7n5qA02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	7n5qF01
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	7n5qF02
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	46.410 Å
Unit-cell length b length_b	61.770 Å
Unit-cell length c length_c	71.680 Å
Unit-cell angle α angle_alpha	111.33 °
Unit-cell angle β angle_beta	91.19 °
Unit-cell angle γ angle_gamma	91.77 °
Molecules per unit cell Z z_pdb	2

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	1.760 Å
Low-resolution limit resolution_low	25.320 Å
R factor r_factor	0.1820
R_work r_work	0.1800
R_free r_free	0.2180

Peptide-MHC complex of mouse H2-Db presenting PA224 with E4C mutation

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

Beta-2-microglobulin

State in the Current Structure

Other States of the Same Protein in the Database

peptide from Polymerase acidic protein

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

7n5q__assembly_1__model_1

7n5q__assembly_1__model_1 | I(q)

7n5q__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

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

Peptide-MHC complex of mouse H2-Db presenting PA224 with E4C mutation

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

peptide from Polymerase acidic 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

7n5q__assembly_1__model_1

7n5q__assembly_1__model_1 | I(q)

7n5q__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

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)