SAXSdb — 9qg8

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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） LYS-THR-MET-MET-ALA-HIS-ASP-LEU × 1 GLYCEROL × 6 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） LYS-THR-MET-MET-ALA-HIS-ASP-LEU × 1 GLYCEROL × 6 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

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	9qg8
Deposition date deposition_date	2025-03-13
Structure title title	Crystal structure of the great reed warbler MHC class I in complex with an 8-mer peptide
Keywords keywords	MHC class I, great reed warbler, antigen presentation, 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.

9qg8__assembly_1__model_1

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

Download this curve (.dat)

9qg8__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9qg8__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	24.30 Å
Rg (electron density)	23.19 Å
Total Rg	24.02 Å
Atom count	3131
Residues	380
Excluded volume	54999 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9qg8__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 (5)

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	3221

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

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

Entity 3 Entity 3 polymer

Description description	LYS-THR-MET-MET-ALA-HIS-ASP-LEU
Molecular weight formula_weight	948.2 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	K

KTMMAHDL

Entity 4 Entity 4 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	85

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Unit-cell length a length_a	205.947 Å
Unit-cell length b length_b	49.038 Å
Unit-cell length c length_c	39.380 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	94.69 °
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	2.150 Å
Low-resolution limit resolution_low	47.700 Å
R factor r_factor	0.2089
R_work r_work	0.2057
R_free r_free	0.2658

Crystal structure of the great reed warbler MHC class I in complex with an 8-mer peptide

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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

9qg8__assembly_1__model_1

9qg8__assembly_1__model_1 | I(q)

9qg8__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 (5)

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 water

7. Citations (1)

Crystal structure of the great reed warbler MHC class I in complex with an 8-mer peptide

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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

9qg8__assembly_1__model_1

9qg8__assembly_1__model_1 | I(q)

9qg8__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 (5)

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 water

7. Citations (1)