[English] 日本語
Yorodumi
- PDB-4wi8: Structural mapping of the human IgG1 binding site for FcRn: hu3S1... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4wi8
TitleStructural mapping of the human IgG1 binding site for FcRn: hu3S193 Fc mutation Y436A
ComponentsIg gamma-1 chain C region
KeywordsIMMUNE SYSTEM / Human IgG1 / FcRn binding site / Therapeutic antibody
Function / homology
Function and homology information


Fc-gamma receptor I complex binding / complement-dependent cytotoxicity / IgG immunoglobulin complex / antibody-dependent cellular cytotoxicity / immunoglobulin receptor binding / immunoglobulin complex, circulating / Classical antibody-mediated complement activation / Initial triggering of complement / FCGR activation / complement activation, classical pathway ...Fc-gamma receptor I complex binding / complement-dependent cytotoxicity / IgG immunoglobulin complex / antibody-dependent cellular cytotoxicity / immunoglobulin receptor binding / immunoglobulin complex, circulating / Classical antibody-mediated complement activation / Initial triggering of complement / FCGR activation / complement activation, classical pathway / Role of phospholipids in phagocytosis / antigen binding / FCGR3A-mediated IL10 synthesis / Regulation of Complement cascade / B cell receptor signaling pathway / FCGR3A-mediated phagocytosis / Regulation of actin dynamics for phagocytic cup formation / antibacterial humoral response / Interleukin-4 and Interleukin-13 signaling / blood microparticle / adaptive immune response / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
: / 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 ...: / 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 / Mainly Beta
Similarity search - Domain/homology
Immunoglobulin heavy constant gamma 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.8 Å
AuthorsFarrugia, W. / Burvenich, I.J.G. / Scott, A.M. / Ramsland, P.A.
Funding support Australia, 2items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)542512 Australia
National Health and Medical Research Council (NHMRC, Australia)1030469 Australia
CitationJournal: To Be Published
Title: Structural and functional mapping of human IgG1 binding site for FcRn in vivo using human FcRn transgenic mice
Authors: Burvenich, I.J.G. / Farrugia, W. / Lee, F.T. / Catimel, B. / Liu, Z. / Makris, D. / Cao, D. / O'Keefe, G. / Brechbiel, M.W. / King, D. / Spirkoska, V. / Allan, L. / Ramsland, P.A. / Scott, A.M.
History
DepositionSep 25, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Data collection / Derived calculations
Category: diffrn_source / pdbx_audit_support / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Jan 8, 2020Group: Author supporting evidence / Data collection / Category: chem_comp / pdbx_audit_support
Item: _chem_comp.type / _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_atoms / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 2.2Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ig gamma-1 chain C region
B: Ig gamma-1 chain C region
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,0305
Polymers47,0852
Non-polymers2,9453
Water81145
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7230 Å2
ΔGint53 kcal/mol
Surface area21970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.109, 79.298, 136.341
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Ig gamma-1 chain C region


Mass: 23542.580 Da / Num. of mol.: 2 / Mutation: Y436A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGHG1 / Cell line (production host): 293F / Production host: Homo sapiens (human) / References: UniProt: P01857
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1463.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-2DManpa1-3[DGlcpNAcb1-2DManpa1-6]DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/4,8,7/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3-1-3-1-4/a4-b1_a6-h1_b4-c1_c3-d1_c6-f1_d2-e1_f2-g1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}}[(6+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}}}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1098.016 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-2DManpa1-3DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3-1-4/a4-b1_a6-f1_b4-c1_c3-d1_d2-e1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}}}}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-beta-D-mannopyranose


Type: oligosaccharide / Mass: 383.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-2DManpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a1122h-1b_1-5][a2122h-1b_1-5_2*NCC/3=O]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-Manp]{[(2+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.66 Å3/Da / Density % sol: 53.69 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: PEG 6000, 0.1 M MES, 25% v/v ethylene glycol

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.954 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 4, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. obs: 13774 / % possible obs: 97.7 % / Redundancy: 5.7 % / Net I/σ(I): 22.6

-
Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.7.3_928) / Classification: refinement
RefinementResolution: 2.8→29.877 Å / SU ML: 0.52 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 30.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2936 1357 10.01 %
Rwork0.2093 --
obs0.2177 13562 99.01 %
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.207 Å2 / ksol: 0.326 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--7.4467 Å2-0 Å20 Å2
2---3.4104 Å2-0 Å2
3---10.8571 Å2
Refinement stepCycle: LAST / Resolution: 2.8→29.877 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3314 0 198 45 3557
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093620
X-RAY DIFFRACTIONf_angle_d1.4154954
X-RAY DIFFRACTIONf_dihedral_angle_d27.4451432
X-RAY DIFFRACTIONf_chiral_restr0.082592
X-RAY DIFFRACTIONf_plane_restr0.006606
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8001-2.90011330.34681193X-RAY DIFFRACTION97
2.9001-3.01610.40931280.28461160X-RAY DIFFRACTION98
3.0161-3.15320.37051340.25921204X-RAY DIFFRACTION99
3.1532-3.31920.34281350.21461214X-RAY DIFFRACTION99
3.3192-3.52690.31071320.21531191X-RAY DIFFRACTION99
3.5269-3.79870.30881360.20551222X-RAY DIFFRACTION99
3.7987-4.18010.29421350.20431210X-RAY DIFFRACTION99
4.1801-4.78280.24281370.17261237X-RAY DIFFRACTION100
4.7828-6.01770.2531400.19181257X-RAY DIFFRACTION100
6.0177-100.25591470.19141317X-RAY DIFFRACTION99
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)
11.8491-0.5066-0.60341.52470.93392.620.1374-0.4885-0.11630.0995-0.1156-0.2380.30130.0131-0.01760.2902-0.0355-0.10440.29430.02220.20679.1727-14.3667-12.576
22.3411-0.5711.09470.9552-0.0861.84370.5981-0.7392-0.9225-0.10720.04990.3170.731-0.0022-0.06080.3414-0.0381-0.10990.58320.10680.655210.3728-18.9053-6.7189
31.4164-0.4703-0.27881.58090.08452.13610.0692-0.43680.31920.18840.07020.0387-0.1575-0.26640.0290.3654-0.0502-0.04470.2975-0.06450.26173.2926-10.7158-12.6211
43.28410.728-0.72082.3322-0.04452.2574-0.20890.48-0.3631-0.06870.3125-0.2552-0.06330.14-0.09930.2195-0.1101-0.06060.2125-0.05140.233221.0289-2.3167-41.455
52.69680.9277-0.94262.1778-0.96971.3695-0.23460.4824-0.6894-0.0440.2863-0.24820.10230.2295-0.06260.185-0.0357-0.04580.2932-0.08890.388320.1407-8.415-40.8561
62.2195-0.5936-0.7071.9440.59841.7762-0.1414-0.36660.38981.36920.37450.48550.0837-0.2657-0.01550.95710.26720.19380.172-0.02010.433534.025612.8314-16.0809
70.85670.2006-1.1210.0549-0.22771.6248-0.8863-0.7646-0.52661.71090.28120.67410.60560.14570.23141.73850.15070.33590.71170.0520.845930.185313.10661.2381
80.7179-0.365-0.36373.8286-0.64860.3745-0.32620.1053-0.13061.6092-0.382-0.3451-0.5217-0.1272-0.19851.50740.1288-0.0970.604-0.01440.555141.773516.4199-5.7483
91.79951.2951-1.2850.9826-1.11321.6141-0.2891-0.37751.26680.51240.25620.06760.037-0.51560.09071.05610.21630.21780.67590.03350.916122.986316.5012-5.6534
103.9503-0.06761.82190.0320.16622.0983-0.4749-0.3955-0.7991.35710.1369-0.6772-0.07020.42270.21330.7490.1271-0.10150.27620.09290.553645.714410.5036-17.9299
110.77970.21050.57940.9819-0.17430.5875-0.3051-0.2999-0.05251.65960.43270.43470.4089-0.10380.59951.75830.43550.04830.6724-0.03320.406935.26897.0246-0.5041
122.56410.90480.32311.93660.27841.6543-0.16840.54490.48260.08540.0146-0.14130.20050.02410.00250.0452-0.0920.01130.2550.1140.327630.44247.5464-39.4194
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 237:279)
2X-RAY DIFFRACTION2chain 'A' and (resseq 280:301)
3X-RAY DIFFRACTION3chain 'A' and (resseq 302:336)
4X-RAY DIFFRACTION4chain 'A' and (resseq 337:372)
5X-RAY DIFFRACTION5chain 'A' and (resseq 373:444)
6X-RAY DIFFRACTION6chain 'B' and (resseq 237:264)
7X-RAY DIFFRACTION7chain 'B' and (resseq 265:279)
8X-RAY DIFFRACTION8chain 'B' and (resseq 280:290)
9X-RAY DIFFRACTION9chain 'B' and (resseq 291:307)
10X-RAY DIFFRACTION10chain 'B' and (resseq 308:318)
11X-RAY DIFFRACTION11chain 'B' and (resseq 319:336)
12X-RAY DIFFRACTION12chain 'B' and (resseq 337:444)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more