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- PDB-4k71: Crystal structure of a high affinity Human Serum Albumin variant ... -

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Basic information

Entry
Database: PDB / ID: 4k71
TitleCrystal structure of a high affinity Human Serum Albumin variant bound to the Neonatal Fc Receptor
Components
  • Beta-2-microglobulin
  • IgG receptor FcRn large subunit p51
  • Serum albumin
KeywordsLIPID TRANSPORT / MHC Class I / Endosome Recycling / Endosome
Function / homology
Function and homology information


IgG immunoglobulin transcytosis in epithelial cells mediated by FcRn immunoglobulin receptor / Ciprofloxacin ADME / exogenous protein binding / cellular response to calcium ion starvation / enterobactin binding / Heme biosynthesis / HDL remodeling / IgG binding / negative regulation of mitochondrial depolarization / Heme degradation ...IgG immunoglobulin transcytosis in epithelial cells mediated by FcRn immunoglobulin receptor / Ciprofloxacin ADME / exogenous protein binding / cellular response to calcium ion starvation / enterobactin binding / Heme biosynthesis / HDL remodeling / IgG binding / negative regulation of mitochondrial depolarization / Heme degradation / Prednisone ADME / Aspirin ADME / beta-2-microglobulin binding / antioxidant activity / toxic substance binding / Scavenging of heme from plasma / Recycling of bile acids and salts / platelet alpha granule lumen / negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / fatty acid binding / DAP12 interactions / cellular response to starvation / transferrin transport / cellular response to iron ion / Endosomal/Vacuolar pathway / Post-translational protein phosphorylation / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide antigen assembly with MHC class II protein complex / cellular response to iron(III) ion / MHC class II protein complex / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / regulation of erythrocyte differentiation / HFE-transferrin receptor complex / response to molecule of bacterial origin / MHC class I peptide loading complex / Cytoprotection by HMOX1 / T cell mediated cytotoxicity / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / MHC class I protein complex / positive regulation of T cell activation / peptide antigen binding / positive regulation of receptor-mediated endocytosis / negative regulation of neurogenesis / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / multicellular organismal-level iron ion homeostasis / specific granule lumen / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / phagocytic vesicle membrane / recycling endosome membrane / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / MHC class II protein complex binding / Modulation by Mtb of host immune system / pyridoxal phosphate binding / late endosome membrane / sensory perception of smell / positive regulation of cellular senescence / tertiary granule lumen / DAP12 signaling / Platelet degranulation / T cell differentiation in thymus / negative regulation of neuron projection development / protein-folding chaperone binding / ER-Phagosome pathway / protein refolding / early endosome membrane / blood microparticle / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / endosome membrane / immune response / endoplasmic reticulum lumen / Amyloid fiber formation / copper ion binding / Golgi membrane / lysosomal membrane / external side of plasma membrane / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity / protein-containing complex / extracellular space / DNA binding
Similarity search - Function
Serum Albumin; Chain A, Domain 1 - #10 / Serum albumin/Alpha-fetoprotein/Afamin / ALB/AFP/VDB / Serum albumin, N-terminal / Serum albumin, conserved site / Serum albumin-like / Serum albumin family / Albumin domain signature. / Albumin domain profile. / serum albumin ...Serum Albumin; Chain A, Domain 1 - #10 / Serum albumin/Alpha-fetoprotein/Afamin / ALB/AFP/VDB / Serum albumin, N-terminal / Serum albumin, conserved site / Serum albumin-like / Serum albumin family / Albumin domain signature. / Albumin domain profile. / serum albumin / Serum Albumin; Chain A, Domain 1 / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / : / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Albumin / IgG receptor FcRn large subunit p51 / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.4 Å
AuthorsSchmidt, M.M. / Townson, S.A. / Andreucci, A. / Dombrowski, C. / Erbe, D.V. / King, B. / Kovalchin, J.T. / Masci, A. / Murillo, A. / Schirmer, E.B. ...Schmidt, M.M. / Townson, S.A. / Andreucci, A. / Dombrowski, C. / Erbe, D.V. / King, B. / Kovalchin, J.T. / Masci, A. / Murillo, A. / Schirmer, E.B. / Furfine, E.S. / Barnes, T.M.
CitationJournal: Structure / Year: 2013
Title: Crystal structure of an HSA/FcRn complex reveals recycling by competitive mimicry of HSA ligands at a pH-dependent hydrophobic interface.
Authors: Schmidt, M.M. / Townson, S.A. / Andreucci, A.J. / King, B.M. / Schirmer, E.B. / Murillo, A.J. / Dombrowski, C. / Tisdale, A.W. / Lowden, P.A. / Masci, A.L. / Kovalchin, J.T. / Erbe, D.V. / ...Authors: Schmidt, M.M. / Townson, S.A. / Andreucci, A.J. / King, B.M. / Schirmer, E.B. / Murillo, A.J. / Dombrowski, C. / Tisdale, A.W. / Lowden, P.A. / Masci, A.L. / Kovalchin, J.T. / Erbe, D.V. / Wittrup, K.D. / Furfine, E.S. / Barnes, T.M.
History
DepositionApr 16, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2014Group: Database references
Revision 1.2Nov 27, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serum albumin
B: IgG receptor FcRn large subunit p51
C: Beta-2-microglobulin
D: Serum albumin
E: IgG receptor FcRn large subunit p51
F: Beta-2-microglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)219,08425
Polymers217,2596
Non-polymers1,82519
Water2,198122
1
A: Serum albumin
B: IgG receptor FcRn large subunit p51
C: Beta-2-microglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,68614
Polymers108,6293
Non-polymers1,05711
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8510 Å2
ΔGint-159 kcal/mol
Surface area44180 Å2
MethodPISA
2
D: Serum albumin
E: IgG receptor FcRn large subunit p51
F: Beta-2-microglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,39811
Polymers108,6293
Non-polymers7698
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7750 Å2
ΔGint-115 kcal/mol
Surface area43960 Å2
MethodPISA
3
A: Serum albumin
B: IgG receptor FcRn large subunit p51
C: Beta-2-microglobulin
hetero molecules

A: Serum albumin
B: IgG receptor FcRn large subunit p51
C: Beta-2-microglobulin
hetero molecules

D: Serum albumin
E: IgG receptor FcRn large subunit p51
F: Beta-2-microglobulin
hetero molecules

D: Serum albumin
E: IgG receptor FcRn large subunit p51
F: Beta-2-microglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)438,16850
Polymers434,51812
Non-polymers3,65038
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation1_554x,y,z-11
crystal symmetry operation2_654-x+1,-y,z-11
Buried area43790 Å2
ΔGint-575 kcal/mol
Surface area165010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.893, 203.536, 100.561
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Serum albumin


Mass: 66473.148 Da / Num. of mol.: 2 / Mutation: V418M, T420A, E505G, V547A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: ALB, GIG20, GIG42, PRO0903, PRO1708, PRO2044, PRO2619, PRO2675, UNQ696/PRO1341
Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P02768
#2: Protein IgG receptor FcRn large subunit p51 / FcRn / IgG Fc fragment receptor transporter alpha chain / Neonatal Fc receptor


Mass: 30408.104 Da / Num. of mol.: 2 / Fragment: UNP residues 24-297
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FCGRT, FCRN / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P55899
#3: Protein Beta-2-microglobulin / Beta-2-microglobulin form pI 5.3


Mass: 11748.160 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P61769
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.07 Å3/Da / Density % sol: 60.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.9
Details: 1.7 M ammonium sulfate, 0.1 M sodium citrate, pH 4.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97872
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 16, 2012
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.4→108.29 Å / Num. obs: 103179 / % possible obs: 99.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Rmerge(I) obs: 0.063
Reflection shellResolution: 2.4→2.59 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.67 / % possible all: 99.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0109refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 2.4→108.29 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.926 / SU B: 18.944 / SU ML: 0.196 / Cross valid method: THROUGHOUT / ESU R: 0.328 / ESU R Free: 0.245 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25513 5144 5 %RANDOM
Rwork0.21201 ---
obs0.21419 97775 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 52.671 Å2
Baniso -1Baniso -2Baniso -3
1--2.21 Å20 Å20 Å2
2--1.98 Å20 Å2
3---0.23 Å2
Refinement stepCycle: LAST / Resolution: 2.4→108.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15042 0 95 122 15259
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.02215298
X-RAY DIFFRACTIONr_bond_other_d0.0020.0210498
X-RAY DIFFRACTIONr_angle_refined_deg1.3961.96520761
X-RAY DIFFRACTIONr_angle_other_deg1.028325481
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.04251881
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.55924.329700
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.062152558
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9931578
X-RAY DIFFRACTIONr_chiral_restr0.0810.22238
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02116965
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023083
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.15229447
X-RAY DIFFRACTIONr_mcbond_other0.58623760
X-RAY DIFFRACTIONr_mcangle_it3.67315155
X-RAY DIFFRACTIONr_scbond_it5.72245851
X-RAY DIFFRACTIONr_scangle_it8.26765606
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.393 366 -
Rwork0.323 7181 -
obs--99.89 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.01880.51560.15521.5330.29062.2281-0.01430.16690.10320.04650.0606-0.1287-0.1190.2396-0.04630.1102-0.00280.02260.0711-0.00280.126555.41345.58225.518
21.16890.7678-0.15675.2285-0.00430.52890.0874-0.121-0.0140.4618-0.14270.52140.0589-0.09620.05540.1207-0.03310.05880.1254-0.05030.107135.03821.29227.91
34.87420.2758-0.7131.5848-0.60451.79010.1474-0.6495-0.1380.3023-0.22850.0320.0963-0.01040.08110.1682-0.07790.00930.1335-0.00950.076561.17815.82728.142
46.2381-0.37540.30573.8688-0.86543.4024-0.0424-0.45530.05350.3244-0.1277-0.5398-0.28770.48710.170.2032-0.01320.01070.17410.0840.226285.26814.03826.41
50.7029-0.4477-0.27341.9010.90532.9323-0.0048-0.11190.088-0.0903-0.04370.2563-0.2356-0.27550.04860.14350.02730.00560.1699-0.00880.192358.851.59474.501
61.98760.6452-0.08693.86881.11182.83910.01440.2791-0.5052-0.34290.0394-0.64790.44210.4312-0.05370.22380.1310.04470.3487-0.06320.292479.19828.07966.181
74.65460.3444-0.64062.03840.94353.24310.04510.9075-0.2036-0.3891-0.0739-0.1490.1055-0.10710.02870.28780.04840.01850.2746-0.06420.106352.97122.79364.779
89.2035-1.40570.18945.43210.86095.09920.07461.0766-0.2072-0.2997-0.43281.1359-0.104-1.20610.35810.3845-0.0439-0.00950.7076-0.26140.360528.81420.41466.207
92.6619-0.06590.45630.5455-0.0710.9829-0.0319-0.03090.1394-0.00260.0243-0.0236-0.1056-0.05870.00760.1205-0.00770.02160.00880.01010.082390.81330.2115.495
102.7079-0.2570.82560.4255-0.02190.7275-0.03060.29940.1096-0.02090.04540.0442-0.0370.125-0.01490.1557-0.010.02090.0906-0.00610.096323.5431.78890.112
113.7316-1.61541.89723.6816-1.65224.09980.08730.2253-0.4832-0.2286-0.1739-0.10970.43780.08960.08660.0719-0.00850.06240.0557-0.02060.2519100.56914.712.011
124.47081.31932.26043.22251.20594.81770.16690.0729-0.60360.0068-0.14210.16620.6081-0.0873-0.02480.17240.011-0.00820.0904-0.04140.278213.72715.83990.268
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 206
2X-RAY DIFFRACTION2A207 - 384
3X-RAY DIFFRACTION3A385 - 490
4X-RAY DIFFRACTION4A491 - 585
5X-RAY DIFFRACTION5D2 - 206
6X-RAY DIFFRACTION6D207 - 384
7X-RAY DIFFRACTION7D385 - 490
8X-RAY DIFFRACTION8D491 - 585
9X-RAY DIFFRACTION9B5 - 175
10X-RAY DIFFRACTION9B176 - 268
11X-RAY DIFFRACTION10E5 - 175
12X-RAY DIFFRACTION10E176 - 268
13X-RAY DIFFRACTION11C1 - 99
14X-RAY DIFFRACTION12F1 - 99

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