6c97

Crystal structure of FcRn at pH3

Method: X-RAY DIFFRACTION Dmax: 97.4 Å Quality: REASONABLE

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

IgG receptor FcRn large subunit p51

Homo sapiens

UniProt P55899

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 × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 24–297 Not recorded Beta-2-microglobulin × 1 (P61769) GOL GLYCEROL × 3 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 3;289 K;APO FCRN CRYSTALS WERE PRODUCED BY SITTING DROP VAPOR DIFFUSION WITH AN EQUAL VOLUME COMBINATION OF THE PROTEIN COMPLEX, PROVIDED IN A PROTEIN SOLUTION CONTAINING 50MM HEPES PH 7.0 AND 75MM NACL, AND AN OPTIMIZATION SCREEN CONTAINING 0.1M CITRIC ACID/NAOH PH 3.01-3.09 AND 12-16% W/V PEG 6,000. Resolution 2.00 Å R-free 0.210
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain C; UniProt 24–297 Not recorded Beta-2-microglobulin × 1 (P61769) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 3;289 K;APO FCRN CRYSTALS WERE PRODUCED BY SITTING DROP VAPOR DIFFUSION WITH AN EQUAL VOLUME COMBINATION OF THE PROTEIN COMPLEX, PROVIDED IN A PROTEIN SOLUTION CONTAINING 50MM HEPES PH 7.0 AND 75MM NACL, AND AN OPTIMIZATION SCREEN CONTAINING 0.1M CITRIC ACID/NAOH PH 3.01-3.09 AND 12-16% W/V PEG 6,000. Resolution 2.00 Å R-free 0.210

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.

30 other PDB entries and 69 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name FCGRN_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–274; UniProt 24–297 Author chain C; PDBConstruct 1–274; UniProt 24–297

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 × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain B; UniProt 21–119 Not recorded IgG receptor FcRn large subunit p51 × 1 (P55899) GOL GLYCEROL × 3 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 3;289 K;APO FCRN CRYSTALS WERE PRODUCED BY SITTING DROP VAPOR DIFFUSION WITH AN EQUAL VOLUME COMBINATION OF THE PROTEIN COMPLEX, PROVIDED IN A PROTEIN SOLUTION CONTAINING 50MM HEPES PH 7.0 AND 75MM NACL, AND AN OPTIMIZATION SCREEN CONTAINING 0.1M CITRIC ACID/NAOH PH 3.01-3.09 AND 12-16% W/V PEG 6,000. Resolution 2.00 Å R-free 0.210
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain D; UniProt 21–119 Not recorded IgG receptor FcRn large subunit p51 × 1 (P55899) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 3;289 K;APO FCRN CRYSTALS WERE PRODUCED BY SITTING DROP VAPOR DIFFUSION WITH AN EQUAL VOLUME COMBINATION OF THE PROTEIN COMPLEX, PROVIDED IN A PROTEIN SOLUTION CONTAINING 50MM HEPES PH 7.0 AND 75MM NACL, AND AN OPTIMIZATION SCREEN CONTAINING 0.1M CITRIC ACID/NAOH PH 3.01-3.09 AND 12-16% W/V PEG 6,000. Resolution 2.00 Å R-free 0.210

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 1997 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name B2MG_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 1–99; UniProt 21–119 Author chain D; PDBConstruct 1–99; 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 6c97

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6c97
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6c97
Deposition date deposition_date2018-01-25
Structure title titleCrystal structure of FcRn at pH3
Keywords keywordsNeonatal Fc Receptor, FcRn, Inhibitor, beta 2 microglobulin, b2m, 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_guinier30.19
Radius of gyration Rg (electron density) rg_electron29.55
Forward intensity I(0) i0105200000.00
Molecular weight molecular_weight80338.0 kDa
Excluded volume excluded_volume99903 ų
Envelope volume envelope_volume124850 ų
Hydration-shell volume shell_volume35380 ų
Envelope diameter envelope_diameter103.0
Shell Rg shell_rg36.63
Envelope Rg envelope_rg29.42
Shape Rg shape_rg29.54
Total Rg total_rg30.24
Total atoms total_atoms5687
Residues n_residues728
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 dmax97.4
Rg (real space) rg_real30.15
Rg uncertainty (real space) rg_real_error0.76
I(0) (real space) i0_real1.0520e+08
I(0) uncertainty (real space) i0_real_error1.9200e+06
Rg (reciprocal space) rg_reciprocal30.17
I(0) (reciprocal space) i0_reciprocal105200000.0000
Solution quality estimate total_estimate0.6999
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary37.5
Skewness Skewness skewness0.296
Kurtosis Kurtosis kurtosis-0.289
Angular range angular_range— – 0.2600 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha15110000.0000
Real-space data points n_real_points53
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.912; Stabil: 1.000; Sysdev: 0.193; Positv: 1.000; Valcen: 0.998; Smooth: 0.782

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_idd6c97a1
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_idd6c97a2
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_idd6c97b_
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_idd6c97c1
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_idd6c97c2
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_idd6c97d_
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)

CATH v4.4 (6 domains)

Domain ID domain_id6c97A01
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_id6c97A02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id6c97B00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id6c97C01
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_id6c97C02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id6c97D00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins

8. Citations (1)

9. Files and Curves (10)