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

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Basic information

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


growth hormone activity / growth hormone receptor complex / prolactin receptor binding / bone maturation / IgG immunoglobulin transcytosis in epithelial cells mediated by FcRn immunoglobulin receptor / animal organ development / positive regulation of multicellular organism growth / Ciprofloxacin ADME / exogenous protein binding / cellular response to calcium ion starvation ...growth hormone activity / growth hormone receptor complex / prolactin receptor binding / bone maturation / IgG immunoglobulin transcytosis in epithelial cells mediated by FcRn immunoglobulin receptor / animal organ development / positive regulation of multicellular organism growth / Ciprofloxacin ADME / exogenous protein binding / cellular response to calcium ion starvation / growth hormone receptor binding / positive regulation of D-glucose transmembrane transport / cell surface receptor signaling pathway via STAT / enterobactin binding / positive regulation of insulin-like growth factor receptor signaling pathway / Heme biosynthesis / HDL remodeling / IgG binding / negative regulation of mitochondrial depolarization / growth hormone receptor signaling pathway / Prednisone ADME / Heme degradation / Aspirin ADME / Prolactin receptor signaling / beta-2-microglobulin binding / antioxidant activity / growth hormone receptor signaling pathway via JAK-STAT / Synthesis, secretion, and deacylation of Ghrelin / cell surface receptor signaling pathway via JAK-STAT / toxic substance binding / Scavenging of heme from plasma / Growth hormone receptor signaling / Recycling of bile acids and salts / positive regulation of MAP kinase activity / : / : / platelet alpha granule lumen / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / negative regulation of receptor binding / DAP12 interactions / cellular response to starvation / fatty acid binding / cytokine activity / endosome lumen / cellular response to iron ion / positive regulation of receptor signaling pathway via JAK-STAT / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / Post-translational protein phosphorylation / peptide antigen assembly with MHC class II protein complex / growth factor activity / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / MHC class II protein complex / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / response to nutrient levels / peptide antigen assembly with MHC class I protein complex / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / response to molecule of bacterial origin / HFE-transferrin receptor complex / cytokine-mediated signaling pathway / T cell mediated cytotoxicity / Cytoprotection by HMOX1 / antigen processing and presentation of endogenous peptide antigen via MHC class I / hormone activity / positive regulation of T cell cytokine production / antigen processing and presentation of exogenous peptide antigen via MHC class II / MHC class I protein complex / positive regulation of immune response / peptide antigen binding / negative regulation of neurogenesis / positive regulation of T cell mediated cytotoxicity / positive regulation of receptor-mediated endocytosis / multicellular organismal-level iron ion homeostasis / positive regulation of T cell activation / cellular response to nicotine / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / Interferon gamma signaling / MHC class II protein complex binding / positive regulation of protein binding / Modulation by Mtb of host immune system / late endosome membrane / pyridoxal phosphate binding / sensory perception of smell / tertiary granule lumen / DAP12 signaling / Platelet degranulation / response to estradiol / protein-folding chaperone binding
Similarity search - Function
Somatotropin / Somatotropin/prolactin / Somatotropin hormone, conserved site / Somatotropin hormone family / Somatotropin, prolactin and related hormones signature 1. / Somatotropin, prolactin and related hormones signature 2. / Serum albumin/Alpha-fetoprotein/Afamin / ALB/AFP/VDB / Serum albumin, N-terminal / Serum albumin, conserved site ...Somatotropin / Somatotropin/prolactin / Somatotropin hormone, conserved site / Somatotropin hormone family / Somatotropin, prolactin and related hormones signature 1. / Somatotropin, prolactin and related hormones signature 2. / 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 / Four-helical cytokine-like, core / 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 / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
CYSTEINE / Somapacitan / Somatotropin / Albumin / IgG receptor FcRn large subunit p51 / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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 / Polymer sequence / Refinement 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_name_com / entity_poly / entity_poly_seq / entity_src_gen / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / refine / struct_asym / struct_conn / struct_ref / struct_ref_seq / struct_ref_seq_dif / 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_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.occupancy / _atom_site.pdbx_formal_charge / _atom_site.type_symbol / _chem_comp.name / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.value / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _refine.pdbx_diffrn_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_site.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_seq_id / _struct_site_gen.auth_asym_id / _struct_site_gen.auth_seq_id / _struct_site_gen.label_asym_id
Revision 2.1Jan 24, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 2.2Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)111,0887
Polymers109,4583
Non-polymers1,6304
Water15,817878
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7210 Å2
ΔGint-11 kcal/mol
Surface area43220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.290, 108.120, 159.530
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 / 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: 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 / Production host: Homo sapiens (human) / Strain (production host): HEK293-6E / References: UniProt: P55899
#3: Protein 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 / Production host: Homo sapiens (human) / Strain (production host): HEK293-6E / References: UniProt: P61769

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Non-polymers , 4 types, 882 molecules

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


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / References: UniProt: P01241*PLUS / Comment: pH buffer*YM
#5: Chemical ChemComp-CYS / CYSTEINE


Type: L-peptide linking / Mass: 121.158 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H7NO2S
#6: 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
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 878 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.46 Å3/Da / Density % sol: 50.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: ammonium acetate, sodium acetate, PEG4000

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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: Jul 9, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→48.85 Å / Num. obs: 95478 / % possible obs: 99.91 % / Redundancy: 6.7 % / Net I/σ(I): 11.23
Reflection shellResolution: 1.95→2.02 Å

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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: 1.95→48.846 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.12 / Phase error: 23.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2262 9143 5 %
Rwork0.1823 --
obs0.1845 182713 99.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.95→48.846 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7575 0 101 878 8554
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0127994
X-RAY DIFFRACTIONf_angle_d1.18710831
X-RAY DIFFRACTIONf_dihedral_angle_d5.9597851
X-RAY DIFFRACTIONf_chiral_restr0.0521148
X-RAY DIFFRACTIONf_plane_restr0.0081410
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-1.97220.35463120.32465834X-RAY DIFFRACTION100
1.9722-1.99540.34722950.30435765X-RAY DIFFRACTION100
1.9954-2.01970.34412900.30055778X-RAY DIFFRACTION100
2.0197-2.04530.31423100.29545787X-RAY DIFFRACTION100
2.0453-2.07220.35893090.30985729X-RAY DIFFRACTION98
2.0722-2.10060.30863050.27185740X-RAY DIFFRACTION100
2.1006-2.13060.28193060.25355845X-RAY DIFFRACTION100
2.1306-2.16240.28863210.24865788X-RAY DIFFRACTION100
2.1624-2.19620.30153000.23685788X-RAY DIFFRACTION100
2.1962-2.23220.27873010.23435826X-RAY DIFFRACTION100
2.2322-2.27070.30992990.26865706X-RAY DIFFRACTION98
2.2707-2.3120.27952880.21595803X-RAY DIFFRACTION100
2.312-2.35650.25423230.20075816X-RAY DIFFRACTION100
2.3565-2.40460.26683040.20075811X-RAY DIFFRACTION100
2.4046-2.45680.25833080.19515765X-RAY DIFFRACTION100
2.4568-2.5140.23523090.1935845X-RAY DIFFRACTION100
2.514-2.57690.25982960.18615797X-RAY DIFFRACTION100
2.5769-2.64650.21453020.18495747X-RAY DIFFRACTION100
2.6465-2.72440.25312980.1785791X-RAY DIFFRACTION99
2.7244-2.81230.20553030.17165728X-RAY DIFFRACTION99
2.8123-2.91280.21663190.1645793X-RAY DIFFRACTION100
2.9128-3.02940.21582970.16515806X-RAY DIFFRACTION100
3.0294-3.16730.22283140.16735799X-RAY DIFFRACTION100
3.1673-3.33420.19982990.15625786X-RAY DIFFRACTION100
3.3342-3.54310.18333080.15385802X-RAY DIFFRACTION100
3.5431-3.81650.19293060.14715777X-RAY DIFFRACTION100
3.8165-4.20040.19033050.14375789X-RAY DIFFRACTION99
4.2004-4.80780.15693110.12355782X-RAY DIFFRACTION100
4.8078-6.05550.19243040.14945761X-RAY DIFFRACTION99
6.0555-48.86110.20593010.18215786X-RAY DIFFRACTION100

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