← Back to search
6kvm

Crystal structure of Chicken MHC Class II for 1.9 angstrom

Method: X-RAY DIFFRACTION Dmax: 85.3 Å Quality: GOOD
▼

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

MHC class II alpha chain

Gallus gallus

UniProt Q4U5Z6

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain A； UniProt 24–217 Not recorded MHC class II beta chain 2 × 1 （Q4U600） peptide from 60S ribosomal protein L30 × 1 （P67883） GOL GLYCEROL × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8.5；291 K；30% PEG 4000, 100mM Tris base/Hydrochloric acid pH 8.5, 200mM Lithium sulfate Resolution 1.90 Å R-free 0.227

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 6KVM Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
6T3Y Improved High Resolution Structure of MHC Class II complex Deposited 2019-10-11 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 27–207（181 aa）
Not recorded GOL GLYCEROL × 3 ACT ACETATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.2 M Na Acetate 0.1 M TRIS 30 %w/v PEG 4K
Resolution 1.70 Å R-free 0.202
6ZWA CLIP peptide bound to chicken MHC class II molecule (BL-2) from B19 haplotype Deposited 2020-07-28 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 27–207（181 aa）
Not recorded PEG DI(HYDROXYETHYL)ETHER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；298 K；0.1 M TRIS pH 8.5, 20.0% w/v PEG 4000, 200mM CaCl2
Resolution 1.68 Å R-free 0.252
7APZ CLIP peptide bound to chicken MHC class II molecule (BL-2) from B2 haplotype with a decamer mode of binding Deposited 2020-10-20 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 27–207（181 aa）
Not recorded IMD IMIDAZOLE × 4 ACE ACETYL GROUP × 20 ZN ZINC ION × 20 PEG DI(HYDROXYETHYL)ETHER × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 NI NICKEL (II) ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.2 M Zinc Acetate (Salt) 0.1 M Imidazole pH 6.5 (Buffer) 10 %w/v PEG 8000 (Precipitant)
Resolution 1.97 Å R-free 0.255
7PDY A viral peptide from Marek's disease virus bound to chicken MHC-II molecule Deposited 2021-08-09 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 27–214（188 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 GOL GLYCEROL × 3 ACT ACETATE ION × 3 PEG DI(HYDROXYETHYL)ETHER × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；293 K；PEG 4000, sodium acetate
Resolution 2.54 Å R-free 0.252
7PDY A viral peptide from Marek's disease virus bound to chicken MHC-II molecule Deposited 2021-08-09 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 27–214（188 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 GOL GLYCEROL × 1 ACT ACETATE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；293 K；PEG 4000, sodium acetate
Resolution 2.54 Å R-free 0.252
7PDY A viral peptide from Marek's disease virus bound to chicken MHC-II molecule Deposited 2021-08-09 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 27–214（188 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 GOL GLYCEROL × 1 ACT ACETATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；293 K；PEG 4000, sodium acetate
Resolution 2.54 Å R-free 0.252

4 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name Q4U5Z6_CHICK
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–194； UniProt 24–217

MHC class II beta chain 2

Gallus gallus

UniProt Q4U600

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain B； UniProt 27–224 Not recorded MHC class II alpha chain × 1 （Q4U5Z6） peptide from 60S ribosomal protein L30 × 1 （P67883） GOL GLYCEROL × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8.5；291 K；30% PEG 4000, 100mM Tris base/Hydrochloric acid pH 8.5, 200mM Lithium sulfate Resolution 1.90 Å R-free 0.227

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence
UniProt name Q4U600_CHICK
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 17–214； UniProt 27–224

peptide from 60S ribosomal protein L30

Gallus gallus

UniProt P67883

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain C； UniProt 99–115 Not recorded MHC class II alpha chain × 1 （Q4U5Z6） MHC class II beta chain 2 × 1 （Q4U600） GOL GLYCEROL × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8.5；291 K；30% PEG 4000, 100mM Tris base/Hydrochloric acid pH 8.5, 200mM Lithium sulfate Resolution 1.90 Å R-free 0.227

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 6KVM Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
8Q7Z Structure of the G. gallus 80S non-rotated ribosome Deposited 2023-08-17 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 80-meric
Chain Bc 1–115（115 aa）
Not recorded MG MAGNESIUM ION × 494 ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.50 Å
8Q87 Structure of the G. gallus 80S rotated ribosome in complex with eEF2 and SERBP1 Deposited 2023-08-18 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 80 PDB declaration: 85-meric
Chain Bc 1–115（115 aa）
Not recorded MG MAGNESIUM ION × 492 ZN ZINC ION × 8 GDP GUANOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.40 Å

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RL30_CHICK
Isoform —
PDB entities 3
Chains and sequence ranges Author chain C； PDBConstruct 1–17； UniProt 99–115

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.

SAXS scattering curve SAXS Profile

SAXS profile for 6kvm

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6kvm
Download Download
▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id6kvm
Deposition date deposition_date2019-09-04
Structure title titleCrystal structure of Chicken MHC Class II for 1.9 angstrom
Keywords keywordsComplex crystal structure MHC class II chicken evolution, IMMUNE SYSTEM; IMMUNE SYSTEM
Experimental Method methodX-RAY DIFFRACTION
▼

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier24.55 Å
Radius of gyration Rg (electron density) rg_electron23.49 Å
Forward intensity I(0) i033621000.00
Molecular weight molecular_weight43945.0 kDa
Excluded volume excluded_volume54575 ų
Envelope volume envelope_volume66684 ų
Hydration-shell volume shell_volume24077 ų
Envelope diameter envelope_diameter87.9 Å
Shell Rg shell_rg30.09 Å
Envelope Rg envelope_rg23.89 Å
Shape Rg shape_rg23.45 Å
Total Rg total_rg24.41 Å
Total atoms total_atoms3107
Residues n_residues380
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax85.3 Å
Rg (real space) rg_real24.58 Å
Rg uncertainty (real space) rg_real_error0.65 Å
I(0) (real space) i0_real3.3620e+07
I(0) uncertainty (real space) i0_real_error4.7550e+05
Rg (reciprocal space) rg_reciprocal24.58 Å
I(0) (reciprocal space) i0_reciprocal33620000.0000
Solution quality estimate total_estimate0.8662
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary28.4 Å
Skewness Skewness skewness0.390
Kurtosis Kurtosis kurtosis-0.280
Angular range angular_range— – 0.3250 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha9372000.0000
Real-space data points n_real_points64
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.804; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.893; Smooth: 0.953
▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (5)

▼

7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd6kvma1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.19 — MHC antigen-recognition domain
Superfamily Superfamily superfamilyd.19.1 — MHC antigen-recognition domain
Family Family familyd.19.1.0 — automated matches
Domain ID domain_idd6kvma2
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.0 — automated matches
Domain ID domain_idd6kvmb1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.19 — MHC antigen-recognition domain
Superfamily Superfamily superfamilyd.19.1 — MHC antigen-recognition domain
Family Family familyd.19.1.0 — automated matches
Domain ID domain_idd6kvmb2
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.0 — automated matches

CATH v4.4 (2 domains)

Domain ID domain_id6kvmA01
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology320 — Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1
Homologous superfamily homologous superfamily10 — Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1
Domain ID domain_id6kvmA02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
▶

8. Citations (1)

▶

9. Files and Curves (10)