SAXSdb — 7zqi

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

MHC class I antigen

Acrocephalus arundinaceus

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 （A0A076JEK1） Inosine monophosphate dehydrogenase-related protein × 1 （Q9KT74） MAGNESIUM ION × 1 CHLORIDE ION × 1 (4S)-2-METHYL-2,4-PENTANEDIOL × 1 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	O98187_ACRAR
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–275； UniProt 26–299

Beta-2-microglobulin

Acrocephalus arundinaceus

UniProt A0A076JEK1

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	MHC class I antigen × 1 （O98187） Inosine monophosphate dehydrogenase-related protein × 1 （Q9KT74） MAGNESIUM ION × 1 CHLORIDE ION × 1 (4S)-2-METHYL-2,4-PENTANEDIOL × 1 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A076JEK1_ACRAR
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 24–122； UniProt 14–112

Inosine monophosphate dehydrogenase-related protein

OrganismNot specified

UniProt Q9KT74

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	MHC class I antigen × 1 （O98187） Beta-2-microglobulin × 1 （A0A076JEK1） MAGNESIUM ION × 1 CHLORIDE ION × 1 (4S)-2-METHYL-2,4-PENTANEDIOL × 1 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9KT74_VIBCH
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain F； PDBConstruct 1–9； UniProt 17–25

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	7zqi
Deposition date deposition_date	2022-04-29
Structure title title	MHC class I from a wild bird in complex with a nonameric peptide P2
Keywords keywords	;Major Histocompatibility Complex Class I, Acrocephalus arundinaceus, antigen presentation, cell-surface receptor, nonameric peptide from Vibrio, 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.

7zqi__assembly_1__model_1

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

Download this curve (.dat)

7zqi__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7zqi__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	24.43 Å
Rg (electron density)	23.34 Å
Total Rg	24.19 Å
Atom count	3161
Residues	390
Excluded volume	55551 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7zqi__assembly_1__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 (7)

Entity 1 Entity 1 polymer

Description description	MHC class I antigen
Molecular weight formula_weight	31630.1 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	3338

MVLHSLHYLDVAVSEPSPGIPQFVAMGFVDGIPFTRYDSERGRMEPLTEWIKDSADPEYWDSQTQIGVGSQHVYARSLETLRERYNQSGGLHTVLRVYGCELLSDGSVRGSERFGYDGRDFISFDLESGRFMAADSAAEITRRRWEHEGIVAERQTNYLKHECPEWLQKYVGYGQKELERKEPPDVHVSGKEEHGTLILSCHAYGFYPKTIAVNWMKGDEIWDQETEWGGVVPNSDGTFHTWARIEALPEEREQYRCRVEHPGMPEPGIFAWEPT

Source Source

Source organism organism	Acrocephalus arundinaceus
Common name common_name	great reed warbler
NCBI taxonomy ID ncbi_taxonomy_id	39621
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	Beta-2-microglobulin
Molecular weight formula_weight	14206.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MHHHHHHSSGVDLGTENLYFQSMAGEAPKVEVYARSRAEEGKENILHCFITGFHPPKIDVELLKNGEPMPGVTYGDLSFNDKWQFQRLVYVPFIPTREDIFTCRVAHSTMPEPRSYRWEPDF

Source Source

Source organism organism	Acrocephalus arundinaceus
Common name common_name	great reed warbler
NCBI taxonomy ID ncbi_taxonomy_id	39621
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 polymer

Description description	Inosine monophosphate dehydrogenase-related protein
Molecular weight formula_weight	1073.3 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	F

YMTLQAVTF

Entity 4 Entity 4 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

Description description	(4S)-2-METHYL-2,4-PENTANEDIOL
Molecular weight formula_weight	118.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	167

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6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id	7zqiA01
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	7zqiA02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	7zqiB01
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	39.202 Å
Unit-cell length b length_b	48.780 Å
Unit-cell length c length_c	202.135 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	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.150 Å
Low-resolution limit resolution_low	50.580 Å
R factor r_factor	0.1825
R_work r_work	0.1798
R_free r_free	0.2294

MHC class I from a wild bird in complex with a nonameric peptide P2

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

MHC class I antigen

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

Inosine monophosphate dehydrogenase-related 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

7zqi__assembly_1__model_1

7zqi__assembly_1__model_1 | I(q)

7zqi__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 (7)

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 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

7. Citations (1)

MHC class I from a wild bird in complex with a nonameric peptide P2

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

MHC class I antigen

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

Inosine monophosphate dehydrogenase-related 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

7zqi__assembly_1__model_1

7zqi__assembly_1__model_1 | I(q)

7zqi__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 (7)

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 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

7. Citations (1)