6qio

Ternary complex of FcRn ectodomain, FcRn binding optimised human serum albumin and the human growth hormone derivative somapacitan

Method: X-RAY DIFFRACTION Dmax: 130.9 Å Quality: GOOD

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

Serum albumin

Homo sapiens

UniProt P02768

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 25–609 Mutation:V418M, T420A, E505G, V547A IgG receptor FcRn large subunit p51 × 1 (P55899) Beta-2-microglobulin × 1 (P61769) MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 CYS CYSTEINE × 2 JG5 Somapacitan × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 5;293 K;ammonium acetate, sodium acetate, PEG4000 Resolution 1.95 Å R-free 0.226

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.

187 other PDB entries and 271 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name ALBU_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–585; UniProt 25–609

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 × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain B; UniProt 24–297 Not recorded Serum albumin × 1 (P02768) Beta-2-microglobulin × 1 (P61769) MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 CYS CYSTEINE × 2 JG5 Somapacitan × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 5;293 K;ammonium acetate, sodium acetate, PEG4000 Resolution 1.95 Å R-free 0.226

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 70 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name FCGRN_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; 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 × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain C; UniProt 21–119 Not recorded Serum albumin × 1 (P02768) IgG receptor FcRn large subunit p51 × 1 (P55899) MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 CYS CYSTEINE × 2 JG5 Somapacitan × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 5;293 K;ammonium acetate, sodium acetate, PEG4000 Resolution 1.95 Å R-free 0.226

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 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 6qio

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id6qio
Deposition date deposition_date2019-01-21
Structure title titleTernary complex of FcRn ectodomain, FcRn binding optimised human serum albumin and the human growth hormone derivative somapacitan
Keywords keywordscomplex, albumin binding, long-acting growth hormone, somapacitan, HORMONE; HORMONE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier34.38
Radius of gyration Rg (electron density) rg_electron33.87
Forward intensity I(0) i0188836000.00
Molecular weight molecular_weight109320.0 kDa
Excluded volume excluded_volume136360 ų
Envelope volume envelope_volume174830 ų
Hydration-shell volume shell_volume43791 ų
Envelope diameter envelope_diameter137.3
Shell Rg shell_rg39.51
Envelope Rg envelope_rg34.18
Shape Rg shape_rg33.84
Total Rg total_rg34.38
Total atoms total_atoms15141
Residues n_residues950
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 dmax130.9
Rg (real space) rg_real34.48
Rg uncertainty (real space) rg_real_error1.52
I(0) (real space) i0_real1.8880e+08
I(0) uncertainty (real space) i0_real_error3.6090e+06
Rg (reciprocal space) rg_reciprocal34.42
I(0) (reciprocal space) i0_reciprocal188800000.0000
Solution quality estimate total_estimate0.8233
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary37.0
Skewness Skewness skewness0.481
Kurtosis Kurtosis kurtosis-0.103
Angular range angular_range— – 0.2300 −1
Current regularization parameter α current_alpha0.0001
Highest regularization parameter α highest_alpha31320000.0000
Real-space data points n_real_points47
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.603; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.898; Smooth: 0.992

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (7)

7. Fold Classification (SCOP + CATH) 11 domains

SCOP 2.08 (8 domains)

Domain ID domain_idd6qioa1
Class classa — All alpha proteins
Fold Fold folda.126 — Serum albumin-like
Superfamily Superfamily superfamilya.126.1 — Serum albumin-like
Family Family familya.126.1.1 — Serum albumin-like
Domain ID domain_idd6qioa2
Class classa — All alpha proteins
Fold Fold folda.126 — Serum albumin-like
Superfamily Superfamily superfamilya.126.1 — Serum albumin-like
Family Family familya.126.1.1 — Serum albumin-like
Domain ID domain_idd6qioa3
Class classa — All alpha proteins
Fold Fold folda.126 — Serum albumin-like
Superfamily Superfamily superfamilya.126.1 — Serum albumin-like
Family Family familya.126.1.1 — Serum albumin-like
Domain ID domain_idd6qiob1
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_idd6qiob2
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_idd6qioc1
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_idd6qioc2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd6qiod_
Class classa — All alpha proteins
Fold Fold folda.26 — 4-helical cytokines
Superfamily Superfamily superfamilya.26.1 — 4-helical cytokines
Family Family familya.26.1.1 — Long-chain cytokines

CATH v4.4 (3 domains)

Domain ID domain_id6qioB01
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_id6qioB02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id6qioC00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins

8. Citations (1)

9. Files and Curves (10)