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- PDB-6qip: Ternary complex of FcRn ectodomain, FcRn binding optimised human ... -

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Basic information

Entry
Database: PDB / ID: 6qip
TitleTernary complex of FcRn ectodomain, FcRn binding optimised human serum albumin and the albumin-biniding side chain of the human growth hormone derivative somapacitan
Components
  • Beta-2-microglobulinBeta-2 microglobulin
  • IgG receptor FcRn large subunit p51
  • Serum albumin
KeywordsTRANSPORT PROTEIN / complex / albumin binding / long-acting growth hormone / somapacitan / HORMONE
Function / homology
Function and homology information


IgG immunoglobulin transcytosis in epithelial cells mediated by FcRn immunoglobulin receptor / cellular response to calcium ion starvation / exogenous protein binding / Ciprofloxacin ADME / HDL remodeling / enterobactin binding / Heme biosynthesis / negative regulation of mitochondrial depolarization / IgG binding / Prednisone ADME ...IgG immunoglobulin transcytosis in epithelial cells mediated by FcRn immunoglobulin receptor / cellular response to calcium ion starvation / exogenous protein binding / Ciprofloxacin ADME / HDL remodeling / enterobactin binding / Heme biosynthesis / negative regulation of mitochondrial depolarization / IgG binding / Prednisone ADME / Heme degradation / antioxidant activity / Aspirin ADME / toxic substance binding / Scavenging of heme from plasma / beta-2-microglobulin binding / Recycling of bile acids and salts / cellular response to starvation / platelet alpha granule lumen / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / early endosome lumen / positive regulation of receptor binding / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / fatty acid binding / Post-translational protein phosphorylation / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / response to molecule of bacterial origin / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / Cytoprotection by HMOX1 / cellular response to iron ion / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / multicellular organismal-level iron ion homeostasis / positive regulation of T cell mediated cytotoxicity / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / MHC class II protein complex / positive regulation of receptor-mediated endocytosis / cellular response to nicotine / recycling endosome membrane / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / phagocytic vesicle membrane / specific granule lumen / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of immune response / negative regulation of epithelial cell proliferation / Modulation by Mtb of host immune system / positive regulation of T cell activation / sensory perception of smell / negative regulation of neuron projection development / pyridoxal phosphate binding / Platelet degranulation / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / late endosome membrane / T cell differentiation in thymus / positive regulation of protein binding / ER-Phagosome pathway / iron ion transport / protein-folding chaperone binding / protein refolding / early endosome membrane / protein homotetramerization / blood microparticle / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / endosome membrane / immune response / copper ion binding / Amyloid fiber formation / lysosomal membrane / endoplasmic reticulum lumen / external side of plasma membrane / Golgi membrane / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / endoplasmic reticulum
Similarity search - Function
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 / MHC class I-like antigen recognition-like ...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 / 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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / CYSTEINE / Somapacitan / Albumin / IgG receptor FcRn large subunit p51 / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsJohansson, E.
CitationJournal: Biochemistry / Year: 2020
Title: Identification of Binding Sites on Human Serum Albumin for Somapacitan, a Long-Acting Growth Hormone Derivative.
Authors: Johansson, E. / Nielsen, A.D. / Demuth, H. / Wiberg, C. / Schjodt, C.B. / Huang, T. / Chen, J. / Jensen, S. / Petersen, J. / Thygesen, P.
History
DepositionJan 21, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 5, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 2.0Sep 20, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / entity_src_gen / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.pdbx_formal_charge / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.gene_src_common_name / _pdbx_struct_assembly_gen.asym_id_list
Revision 2.1Jan 24, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,0457
Polymers109,4583
Non-polymers1,5874
Water46826
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6980 Å2
ΔGint-12 kcal/mol
Surface area44510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.020, 114.450, 159.350
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 3 types, 3 molecules ABC

#1: Protein Serum albumin /


Mass: 66473.148 Da / Num. of mol.: 1
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: Komagataella pastoris (fungus) / 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.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FCGRT, FCRN / Cell line (production host): HEK293-6E / Production host: Homo sapiens (human) / References: UniProt: P55899
#3: Protein Beta-2-microglobulin / Beta-2 microglobulin


Mass: 12577.041 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Cell line (production host): HEK293-6E / Production host: Homo sapiens (human) / References: UniProt: P61769

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Non-polymers , 5 types, 30 molecules

#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Chemical ChemComp-JG5 / Somapacitan / (2S)-6-acetamido-2-[[2-[2-[2-[[4-carboxy-4-[[(4S)-4-carboxy-4-[[2-[2-[2-[4-[16-(1H-tetrazol-5-yl)hexadecanoylsulfamoyl]butanoylamino]ethoxy]ethoxy]acetyl]amino]butanoyl]amino]butanoyl]amino]ethoxy]ethoxy]acetyl]amino]hexanoic acid


Mass: 1192.380 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C51H89N11O19S
#6: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL / 2-Mercaptoethanol


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#7: Chemical ChemComp-CYS / CYSTEINE / Cysteine


Type: L-peptide linking / Mass: 121.158 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C3H7NO2S
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Formula: H2O

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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: 3.2 Å3/Da / Density % sol: 61.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: sodium cacodylate, PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 9, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.45→44.14 Å / Num. obs: 52497 / % possible obs: 99.91 % / Redundancy: 6.6 % / Biso Wilson estimate: 58.05 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.08365 / Rpim(I) all: 0.03514 / Rrim(I) all: 0.09086 / Net I/σ(I): 17.08
Reflection shellResolution: 2.45→2.538 Å / Redundancy: 6.4 % / Rmerge(I) obs: 1.683 / Mean I/σ(I) obs: 1.12 / Num. unique obs: 5168 / CC1/2: 0.585 / Rpim(I) all: 0.7175 / Rrim(I) all: 1.831 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4K71

4k71


Resolution: 2.45→46.479 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.1 / Phase error: 31.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2585 5002 5.01 %
Rwork0.2161 --
obs0.2182 99876 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.45→46.479 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7559 0 104 26 7689
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0117900
X-RAY DIFFRACTIONf_angle_d1.50410686
X-RAY DIFFRACTIONf_dihedral_angle_d5.6827809
X-RAY DIFFRACTIONf_chiral_restr0.081133
X-RAY DIFFRACTIONf_plane_restr0.011385
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.45-2.47790.45621740.43193162X-RAY DIFFRACTION100
2.4779-2.5070.41711950.42973120X-RAY DIFFRACTION100
2.507-2.53760.42831650.39693154X-RAY DIFFRACTION100
2.5376-2.56970.34471540.37723234X-RAY DIFFRACTION100
2.5697-2.60350.32291580.34693149X-RAY DIFFRACTION100
2.6035-2.63920.3381590.34883090X-RAY DIFFRACTION100
2.6392-2.67690.38311860.32513174X-RAY DIFFRACTION100
2.6769-2.71680.33281600.30763157X-RAY DIFFRACTION100
2.7168-2.75930.31881510.29583208X-RAY DIFFRACTION100
2.7593-2.80450.32771630.27723155X-RAY DIFFRACTION100
2.8045-2.85290.33821610.27093182X-RAY DIFFRACTION100
2.8529-2.90480.33731580.28473143X-RAY DIFFRACTION100
2.9048-2.96060.34711660.27673169X-RAY DIFFRACTION100
2.9606-3.0210.37911730.2723150X-RAY DIFFRACTION100
3.021-3.08670.3281670.2693202X-RAY DIFFRACTION100
3.0867-3.15850.27831660.26643156X-RAY DIFFRACTION100
3.1585-3.23750.30421640.24993137X-RAY DIFFRACTION100
3.2375-3.3250.28641890.24843170X-RAY DIFFRACTION100
3.325-3.42280.32671530.24693157X-RAY DIFFRACTION100
3.4228-3.53320.33231700.22823194X-RAY DIFFRACTION100
3.5332-3.65950.24581650.2293160X-RAY DIFFRACTION100
3.6595-3.80590.23641380.22123176X-RAY DIFFRACTION100
3.8059-3.9790.23891910.20413137X-RAY DIFFRACTION100
3.979-4.18870.23991760.18913167X-RAY DIFFRACTION100
4.1887-4.45090.22631720.17193180X-RAY DIFFRACTION100
4.4509-4.79430.19091620.15713170X-RAY DIFFRACTION100
4.7943-5.27610.21661640.16323141X-RAY DIFFRACTION100
5.2761-6.03820.19661680.18583166X-RAY DIFFRACTION100
6.0382-7.60210.24571670.18063171X-RAY DIFFRACTION100
7.6021-46.48740.17961670.14443143X-RAY DIFFRACTION100

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