[English] 日本語
Yorodumi
- PDB-8din: The complex structure between human IgG1 Fc and its high affinity... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8din
TitleThe complex structure between human IgG1 Fc and its high affinity receptor FcgRI H174R variant
Components
  • High affinity immunoglobulin gamma Fc receptor I
  • Ig gamma-1 Fc chain
KeywordsIMMUNE SYSTEM / High affinity IgG1 Fc receptor
Function / homology
Function and homology information


high-affinity IgG receptor activity / IgG receptor activity / positive regulation of type III hypersensitivity / Fc-gamma receptor signaling pathway / phagocytosis, recognition / positive regulation of type IIa hypersensitivity / Fc-gamma receptor I complex binding / complement-dependent cytotoxicity / IgG immunoglobulin complex / antibody-dependent cellular cytotoxicity ...high-affinity IgG receptor activity / IgG receptor activity / positive regulation of type III hypersensitivity / Fc-gamma receptor signaling pathway / phagocytosis, recognition / positive regulation of type IIa hypersensitivity / Fc-gamma receptor I complex binding / complement-dependent cytotoxicity / IgG immunoglobulin complex / antibody-dependent cellular cytotoxicity / IgG binding / Cross-presentation of soluble exogenous antigens (endosomes) / Classical antibody-mediated complement activation / Initial triggering of complement / phagocytosis, engulfment / immunoglobulin complex, circulating / immunoglobulin receptor binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / FCGR activation / Role of phospholipids in phagocytosis / complement activation, classical pathway / positive regulation of phagocytosis / antigen binding / receptor-mediated endocytosis / FCGR3A-mediated IL10 synthesis / Regulation of Complement cascade / FCGR3A-mediated phagocytosis / B cell receptor signaling pathway / clathrin-coated endocytic vesicle membrane / Regulation of actin dynamics for phagocytic cup formation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / antibacterial humoral response / early endosome membrane / Interleukin-4 and Interleukin-13 signaling / blood microparticle / adaptive immune response / cell surface receptor signaling pathway / defense response to bacterium / immune response / external side of plasma membrane / innate immune response / signal transduction / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
: / Immunoglobulin domain / Immunoglobulin / Immunoglobulin domain / Immunoglobulin domain / : / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin subtype / Immunoglobulin ...: / Immunoglobulin domain / Immunoglobulin / Immunoglobulin domain / Immunoglobulin domain / : / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin subtype / Immunoglobulin / 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
Similarity search - Domain/homology
Immunoglobulin heavy constant gamma 1 / High affinity immunoglobulin gamma Fc receptor I
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsLu, J. / Sun, P.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)Division of ntramural research United States
CitationJournal: Front Immunol / Year: 2023
Title: Fc gamma RI FG-loop functions as a pH sensitive switch for IgG binding and release.
Authors: Lu, J. / Spencer, M. / Zou, Z. / Traver, M. / Brzostowski, J. / Sun, P.D.
History
DepositionJun 29, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 10, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Ig gamma-1 Fc chain
A: Ig gamma-1 Fc chain
C: High affinity immunoglobulin gamma Fc receptor I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,8756
Polymers80,5993
Non-polymers3,2753
Water2,288127
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10890 Å2
ΔGint46 kcal/mol
Surface area35430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)203.997, 88.804, 55.925
Angle α, β, γ (deg.)90.000, 98.050, 90.000
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Ig gamma-1 Fc chain / IgG1 Fc


Mass: 24698.955 Da / Num. of mol.: 2 / Fragment: CH2 and CH3 regions, residues 112-330
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGHG1 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P01857
#2: Protein High affinity immunoglobulin gamma Fc receptor I / IgG Fc receptor I / Fc-gamma RI / FcRI / Fc-gamma RIA / FcgammaRIa


Mass: 31201.312 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FCGR1A, FCG1, FCGR1, IGFR1 / Production host: Escherichia coli (E. coli) / References: UniProt: P12314
#3: Polysaccharide beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose- ...beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[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: 1625.490 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpb1-4DGlcpNAcb1-2DManpa1-6[DGlcpNAcb1-2DManpa1-3]DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/5,9,8/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a2112h-1b_1-5][a1221m-1a_1-5]/1-1-2-3-1-3-1-4-5/a4-b1_a6-i1_b4-c1_c3-d1_c6-f1_d2-e1_f2-g1_g4-h1WURCSPDB2Glycan 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-D-Manp]{[(2+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{}}}}}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 127 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.12 Å3/Da / Density % sol: 60.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 20% PEG3350, 0.2M Magnesium formate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 3, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.48→50 Å / Num. obs: 34744 / % possible obs: 98.2 % / Redundancy: 5.3 % / Biso Wilson estimate: 50.44 Å2 / Rmerge(I) obs: 0.118 / Net I/σ(I): 14.1
Reflection shellResolution: 2.48→2.53 Å / Rmerge(I) obs: 0.579 / Num. unique obs: 2137 / % possible all: 97.8

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
PHENIX1.20.1_4487refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4x4m

4x4m


Resolution: 2.5→36.77 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2231 1704 5.01 %
Rwork0.1769 32277 -
obs0.1793 33981 98.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 269.99 Å2 / Biso mean: 68.2631 Å2 / Biso min: 22.73 Å2
Refinement stepCycle: final / Resolution: 2.5→36.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5488 0 221 127 5836
Biso mean--78.35 50.77 -
Num. residues----691
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5-2.570.36521320.28892601273396
2.57-2.660.29971380.23192656279498
2.66-2.750.28311290.21512657278699
2.75-2.860.29271340.22262666280099
2.86-2.990.26021470.211327162863100
2.99-3.150.2671340.202726722806100
3.15-3.350.2431550.191327142869100
3.35-3.60.2291380.186426962834100
3.6-3.970.22051500.17142700285099
3.97-4.540.21291590.145627062865100
4.54-5.720.16411420.14227222864100
5.72-36.770.18731460.16342771291799
Refinement TLS params.Method: refined / Origin x: 30.324 Å / Origin y: -47.271 Å / Origin z: 63.3438 Å
111213212223313233
T0.2561 Å2-0.0054 Å20.0049 Å2-0.2543 Å2-0.0199 Å2--0.2759 Å2
L0.3085 °2-0.1918 °20.2553 °2-0.3455 °2-0.2622 °2--0.5644 °2
S0.0068 Å °0.0402 Å °0.027 Å °-0.0087 Å °0.0072 Å °0.006 Å °0.0666 Å °0.0244 Å °-0 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allB231 - 445
2X-RAY DIFFRACTION1allB501 - 509
3X-RAY DIFFRACTION1allA232 - 509
4X-RAY DIFFRACTION1allC19 - 280
5X-RAY DIFFRACTION1allS1 - 129
6X-RAY DIFFRACTION1allD1

+
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