6mpp

HLA-A*01:01 complex with NRAS Q61K peptide by NMR

Method: SOLUTION NMR Dmax: 73.8 Å Quality: REASONABLE

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

HLA class I histocompatibility antigen, A-1 alpha chain

Homo sapiens

UniProt P30443

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 25–303 Fragment:residues 25-303 NRAS Q61K peptide × 1 Beta-2-microglobulin × 1 (P61769) SOLUTION NMR NMR measurement conditions:pH 7.2;298 K;Ionic strength (raw mmCIF value) 20;Pressure 1 NMR sample composition:300 uM [U-99% 13C; U-99% 15N] MHC-I HLA-A01:01, 300 uM NRAS Q16K, 300 uM Hb2M, 90% H2O/10% D2O | 90% H2O/10% D2O NMR sample composition:180 uM [U-15N; U-2H]; [U-15N; U-2H; Methyl-1H; Methyl-13C]-Ala, Ile, Leu & Val MHC-I HLA-A01:01, 180 uM NRAS Q16K, 180 uM Hb2M, 90% H2O/10% D2O | 90% H2O/10% D2O NMR sample composition:210 uM [U-15N; U-2H]; [U-15N; U-2H; Methyl-1H; Methyl-13C]-Ala, Ile, Leu & Val; [U-13C; U-15N]-Phe & Tyr MHC-I HLA-A01:01, 210 uM [U-15N] NRAS Q16K, 210 uM [U-2H] Hb2M, 90% H2O/10% D2O | 90% H2O/10% D2O NMR sample composition:170 uM [U-15N; U-2H]; [U-15N; U-2H; Methyl-1H; Methyl-13C]-Ala, Ile, Leu & Val MHC-I HLA-A01:01, 170 uM NRAS Q16K, 170 uM Hb2M, 100% D2O | 100% D2O Resolution not provided

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.

7 other PDB entries and 18 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name 1A01_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–279; UniProt 25–303

Beta-2-microglobulin

Homo sapiens

UniProt P61769

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 21–119 Not recorded HLA class I histocompatibility antigen, A-1 alpha chain × 1 (P30443) NRAS Q61K peptide × 1 SOLUTION NMR NMR measurement conditions:pH 7.2;298 K;Ionic strength (raw mmCIF value) 20;Pressure 1 NMR sample composition:300 uM [U-99% 13C; U-99% 15N] MHC-I HLA-A01:01, 300 uM NRAS Q16K, 300 uM Hb2M, 90% H2O/10% D2O | 90% H2O/10% D2O NMR sample composition:180 uM [U-15N; U-2H]; [U-15N; U-2H; Methyl-1H; Methyl-13C]-Ala, Ile, Leu & Val MHC-I HLA-A01:01, 180 uM NRAS Q16K, 180 uM Hb2M, 90% H2O/10% D2O | 90% H2O/10% D2O NMR sample composition:210 uM [U-15N; U-2H]; [U-15N; U-2H; Methyl-1H; Methyl-13C]-Ala, Ile, Leu & Val; [U-13C; U-15N]-Phe & Tyr MHC-I HLA-A01:01, 210 uM [U-15N] NRAS Q16K, 210 uM [U-2H] Hb2M, 90% H2O/10% D2O | 90% H2O/10% D2O NMR sample composition:170 uM [U-15N; U-2H]; [U-15N; U-2H; Methyl-1H; Methyl-13C]-Ala, Ile, Leu & Val MHC-I HLA-A01:01, 170 uM NRAS Q16K, 170 uM Hb2M, 100% D2O | 100% D2O Resolution not provided

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.

1313 other PDB entries and 1998 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name B2MG_HUMAN
Isoform
PDB entities 3
Chains and sequence ranges Author chain C; PDBConstruct 2–100; UniProt 21–119

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 6mpp

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6mpp
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6mpp
Deposition date deposition_date2018-10-08
Structure title titleHLA-A*01:01 complex with NRAS Q61K peptide by NMR
Keywords keywordsIMMUNE SYSTEM; IMMUNE SYSTEM
Experimental Method methodSOLUTION NMR

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

Radius of gyration Rg (Guinier) rg_guinier23.80
Radius of gyration Rg (electron density) rg_electron23.27
Forward intensity I(0) i03008300000.00
Molecular weight molecular_weight445650.0 kDa
Excluded volume excluded_volume548420 ų
Envelope volume envelope_volume69932 ų
Hydration-shell volume shell_volume25065 ų
Envelope diameter envelope_diameter78.3
Shell Rg shell_rg30.23
Envelope Rg envelope_rg23.44
Shape Rg shape_rg23.25
Total Rg total_rg23.42
Total atoms total_atoms61100
Residues n_residues3840
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −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 dmax73.8
Rg (real space) rg_real23.74
Rg uncertainty (real space) rg_real_error0.39
I(0) (real space) i0_real3.0080e+09
I(0) uncertainty (real space) i0_real_error4.0900e+07
Rg (reciprocal space) rg_reciprocal23.76
I(0) (reciprocal space) i0_reciprocal3008000000.0000
Solution quality estimate total_estimate0.7446
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary30.0
Skewness Skewness skewness0.239
Kurtosis Kurtosis kurtosis-0.510
Angular range angular_range— – 0.3350 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha6949000.0000
Real-space data points n_real_points65
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.961; Stabil: 1.000; Sysdev: 0.286; Positv: 1.000; Valcen: 0.996; Smooth: 0.939

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 7 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd6mppa1
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.19.1.1 — MHC antigen-recognition domain
Domain ID domain_idd6mppa2
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_idd6mppc1
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.2 — C1 set domains (antibody constant domain-like)
Domain ID domain_idd6mppc2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (3 domains)

Domain ID domain_id6mppA01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology500 — Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1
Homologous superfamily homologous superfamily10 — MHC class I-like antigen recognition-like
Domain ID domain_id6mppA02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id6mppC00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins

8. Citations (1)

9. Files and Curves (10)