4k71

Crystal structure of a high affinity Human Serum Albumin variant bound to the Neonatal Fc Receptor

Method: X-RAY DIFFRACTION Dmax: 171.4 Å Quality: REASONABLE

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) SO4 SULFATE ION × 11 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 4.9;293 K;1.7 M ammonium sulfate, 0.1 M sodium citrate, pH 4.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.40 Å R-free 0.255
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain D; UniProt 25–609 Mutation:V418M, T420A, E505G, V547A IgG receptor FcRn large subunit p51 × 1 (P55899) Beta-2-microglobulin × 1 (P61769) SO4 SULFATE ION × 8 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 4.9;293 K;1.7 M ammonium sulfate, 0.1 M sodium citrate, pH 4.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.40 Å R-free 0.255
3 Protein heterocomplex Heteromer Protein × 12 PDB declaration: dodecameric(12) Consistent with protein copy count Chain A; UniProt 25–609 Chain D; UniProt 25–609 Mutation:V418M, T420A, E505G, V547A IgG receptor FcRn large subunit p51 × 4 (P55899) Beta-2-microglobulin × 4 (P61769) SO4 SULFATE ION × 38 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 4.9;293 K;1.7 M ammonium sulfate, 0.1 M sodium citrate, pH 4.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.40 Å R-free 0.255

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 269 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 Author chain D; 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 Fragment:UNP residues 24-297 Serum albumin × 1 (P02768) Beta-2-microglobulin × 1 (P61769) SO4 SULFATE ION × 11 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 4.9;293 K;1.7 M ammonium sulfate, 0.1 M sodium citrate, pH 4.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.40 Å R-free 0.255
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain E; UniProt 24–297 Fragment:UNP residues 24-297 Serum albumin × 1 (P02768) Beta-2-microglobulin × 1 (P61769) SO4 SULFATE ION × 8 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 4.9;293 K;1.7 M ammonium sulfate, 0.1 M sodium citrate, pH 4.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.40 Å R-free 0.255
3 Protein heterocomplex Heteromer Protein × 12 PDB declaration: dodecameric(12) Consistent with protein copy count Chain B; UniProt 24–297 Chain E; UniProt 24–297 Fragment:UNP residues 24-297 Serum albumin × 4 (P02768) Beta-2-microglobulin × 4 (P61769) SO4 SULFATE ION × 38 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 4.9;293 K;1.7 M ammonium sulfate, 0.1 M sodium citrate, pH 4.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.40 Å R-free 0.255

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 68 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 Author chain E; 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) SO4 SULFATE ION × 11 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 4.9;293 K;1.7 M ammonium sulfate, 0.1 M sodium citrate, pH 4.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.40 Å R-free 0.255
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain F; UniProt 21–119 Not recorded Serum albumin × 1 (P02768) IgG receptor FcRn large subunit p51 × 1 (P55899) SO4 SULFATE ION × 8 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 4.9;293 K;1.7 M ammonium sulfate, 0.1 M sodium citrate, pH 4.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.40 Å R-free 0.255
3 Protein heterocomplex Heteromer Protein × 12 PDB declaration: dodecameric(12) Consistent with protein copy count Chain C; UniProt 21–119 Chain F; UniProt 21–119 Not recorded Serum albumin × 4 (P02768) IgG receptor FcRn large subunit p51 × 4 (P55899) SO4 SULFATE ION × 38 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 4.9;293 K;1.7 M ammonium sulfate, 0.1 M sodium citrate, pH 4.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.40 Å R-free 0.255

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 1996 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 Author chain F; 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 4k71

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4k71
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4k71
Deposition date deposition_date2013-04-16
Structure title titleCrystal structure of a high affinity Human Serum Albumin variant bound to the Neonatal Fc Receptor
Keywords keywordsMHC Class I, Lipid Transport, Endosome Recycling, Endosome; LIPID TRANSPORT
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier46.36
Radius of gyration Rg (electron density) rg_electron46.48
Forward intensity I(0) i0713158000.00
Molecular weight molecular_weight215890.0 kDa
Excluded volume excluded_volume268300 ų
Envelope volume envelope_volume372350 ų
Hydration-shell volume shell_volume69701 ų
Envelope diameter envelope_diameter183.0
Shell Rg shell_rg47.89
Envelope Rg envelope_rg46.16
Shape Rg shape_rg46.52
Total Rg total_rg46.39
Total atoms total_atoms15137
Residues n_residues1888
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 dmax171.4
Rg (real space) rg_real46.64
Rg uncertainty (real space) rg_real_error1.83
I(0) (real space) i0_real7.1320e+08
I(0) uncertainty (real space) i0_real_error1.4130e+07
Rg (reciprocal space) rg_reciprocal46.36
I(0) (reciprocal space) i0_reciprocal712900000.0000
Solution quality estimate total_estimate0.6377
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary50.4
Skewness Skewness skewness0.537
Kurtosis Kurtosis kurtosis0.018
Angular range angular_range— – 0.1700 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha89430000.0000
Real-space data points n_real_points35
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.685; Stabil: 1.000; Sysdev: 0.115; Positv: 1.000; Valcen: 0.970; Smooth: 0.916

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 30 domains

SCOP 2.08 (12 domains)

Domain ID domain_idd4k71a1
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_idd4k71a2
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_idd4k71a3
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_idd4k71b1
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_idd4k71b2
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_idd4k71c_
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_idd4k71d1
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_idd4k71d2
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_idd4k71d3
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_idd4k71e1
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_idd4k71e2
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_idd4k71f_
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 (18 domains)

Domain ID domain_id4k71A01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology246 — Serum Albumin; Chain A, Domain 1
Homologous superfamily homologous superfamily10
Domain ID domain_id4k71A02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology246 — Serum Albumin; Chain A, Domain 1
Homologous superfamily homologous superfamily10
Domain ID domain_id4k71A03
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology246 — Serum Albumin; Chain A, Domain 1
Homologous superfamily homologous superfamily10
Domain ID domain_id4k71A04
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology246 — Serum Albumin; Chain A, Domain 1
Homologous superfamily homologous superfamily10
Domain ID domain_id4k71A05
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology246 — Serum Albumin; Chain A, Domain 1
Homologous superfamily homologous superfamily10
Domain ID domain_id4k71A06
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology246 — Serum Albumin; Chain A, Domain 1
Homologous superfamily homologous superfamily10
Domain ID domain_id4k71B01
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_id4k71B02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id4k71C00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id4k71D01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology246 — Serum Albumin; Chain A, Domain 1
Homologous superfamily homologous superfamily10
Domain ID domain_id4k71D02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology246 — Serum Albumin; Chain A, Domain 1
Homologous superfamily homologous superfamily10
Domain ID domain_id4k71D03
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology246 — Serum Albumin; Chain A, Domain 1
Homologous superfamily homologous superfamily10
Domain ID domain_id4k71D04
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology246 — Serum Albumin; Chain A, Domain 1
Homologous superfamily homologous superfamily10
Domain ID domain_id4k71D05
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology246 — Serum Albumin; Chain A, Domain 1
Homologous superfamily homologous superfamily10
Domain ID domain_id4k71D06
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology246 — Serum Albumin; Chain A, Domain 1
Homologous superfamily homologous superfamily10
Domain ID domain_id4k71E01
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_id4k71E02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id4k71F00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins

8. Citations (1)

9. Files and Curves (10)