[English] 日本語
Yorodumi
- PDB-2gj7: Crystal Structure of a gE-gI/Fc complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2gj7
TitleCrystal Structure of a gE-gI/Fc complex
Components
  • Glycoprotein E
  • Ig gamma-1 chain C region
KeywordsIMMUNE SYSTEM/VIRUS/VIRAL PROTEIN / Fc receptor / low resolution / IMMUNE SYSTEM-VIRUS-VIRAL PROTEIN COMPLEX
Function / homology
Function and homology information


host cell junction / complement-dependent cytotoxicity / antibody-dependent cellular cytotoxicity / Fc-gamma receptor I complex binding / Classical antibody-mediated complement activation / IgG immunoglobulin complex / Initial triggering of complement / host cell Golgi membrane / FCGR activation / Role of phospholipids in phagocytosis ...host cell junction / complement-dependent cytotoxicity / antibody-dependent cellular cytotoxicity / Fc-gamma receptor I complex binding / Classical antibody-mediated complement activation / IgG immunoglobulin complex / Initial triggering of complement / host cell Golgi membrane / FCGR activation / Role of phospholipids in phagocytosis / immunoglobulin complex, circulating / immunoglobulin receptor binding / complement activation, classical pathway / FCGR3A-mediated IL10 synthesis / host cell endosome membrane / antigen binding / Regulation of Complement cascade / FCGR3A-mediated phagocytosis / B cell receptor signaling pathway / Regulation of actin dynamics for phagocytic cup formation / antibacterial humoral response / Interleukin-4 and Interleukin-13 signaling / adaptive immune response / blood microparticle / virus-mediated perturbation of host defense response / viral envelope / virion membrane / extracellular space / extracellular exosome / extracellular region / membrane / identical protein binding / plasma membrane
Similarity search - Function
Envelope glycoprotein E, Fc-binding domain / Envelope glycoprotein E, N-terminal / Alphaherpesvirus glycoprotein E / Alphaherpesvirus glycoprotein E N-terminal / 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. ...Envelope glycoprotein E, Fc-binding domain / Envelope glycoprotein E, N-terminal / Alphaherpesvirus glycoprotein E / Alphaherpesvirus glycoprotein E N-terminal / 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 / Envelope glycoprotein E
Similarity search - Component
Biological speciesHomo sapiens (human)
Human herpesvirus 1 (Herpes simplex virus type 1)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement, MIRAS / MIRAS / Resolution: 5 Å
AuthorsSprague, E.R. / Wang, C. / Baker, D. / Bjorkman, P.J.
CitationJournal: Plos Biol. / Year: 2006
Title: Crystal Structure of the HSV-1 Fc Receptor Bound to Fc Reveals a Mechanism for Antibody Bipolar Bridging.
Authors: Sprague, E.R. / Wang, C. / Baker, D. / Bjorkman, P.J.
History
DepositionMar 30, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 30, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / 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 / pdbx_validate_chiral / struct_asym / struct_conn / 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_comp_id / _atom_site.label_asym_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_chiral.auth_asym_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 6, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)140,0596
Polymers137,2154
Non-polymers2,8452
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)174.726, 174.726, 315.997
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
DetailsThe asymmetric unit contains one biological complex (1 Fc dimer and 2 gE-gI heterodimers).

-
Components

#1: Protein Ig gamma-1 chain C region


Mass: 25611.021 Da / Num. of mol.: 2 / Fragment: Fc fragment
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IgG1 heavy chain / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P01857
#2: Protein Glycoprotein E


Mass: 42996.254 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human herpesvirus 1 (Herpes simplex virus type 1)
Genus: Simplexvirus / Strain: KOS / Gene: GE, US8 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P04488
#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)-[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: 1422.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpb1-4DGlcpNAcb1-2DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/5,8,7/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a2112h-1b_1-5][a1221m-1a_1-5]/1-1-2-3-3-1-4-5/a4-b1_a6-h1_b4-c1_c3-d1_c6-e1_e2-f1_f4-g1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{}}}}}[(6+1)][b-L-Fucp]{}}}LINUCSPDB-CARE

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 5

-
Sample preparation

CrystalDensity Matthews: 5.71 Å3/Da / Density % sol: 78.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.9-1.1 M sodium malonate, 0.1 M Hepes or 0.1 M MES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31001
41001
51001
1,2,3,4,51
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRL BL9-110.9537
SYNCHROTRONSSRL BL9-221.1048
SYNCHROTRONSSRL BL9-231.0717
SYNCHROTRONSSRL BL9-241.006
SYNCHROTRONSSRL BL9-251.214
Detector
TypeIDDetectorDate
MAR scanner 345 mm plate1IMAGE PLATEMay 16, 2002
MARMOSAIC 325 mm CCD2CCDMay 25, 2005
MARMOSAIC 325 mm CCD3CCDJul 6, 2005
MARMOSAIC 325 mm CCD4CCDJul 6, 2005
MARMOSAIC 325 mm CCD5CCDJul 6, 2005
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1MIRRORSSINGLE WAVELENGTHMx-ray1
2Double crystal monochromatorSINGLE WAVELENGTHMx-ray1
3Double crystal monochromatorSINGLE WAVELENGTHMx-ray1
4Double crystal monochromatorSINGLE WAVELENGTHMx-ray1
5Double crystal monochromatorSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.95371
21.10481
31.07171
41.0061
51.2141
ReflectionResolution: 5→36 Å / Num. all: 21938 / Num. obs: 21931 / % possible obs: 99.7 % / Observed criterion σ(I): 1 / Redundancy: 11.2 % / Rmerge(I) obs: 0.106 / Net I/σ(I): 21.3
Reflection shellResolution: 5→5.27 Å / Redundancy: 10.6 % / Rmerge(I) obs: 0.708 / Mean I/σ(I) obs: 4.2 / % possible all: 100

-
Phasing

PhasingMethod: MIRAS
Phasing setD res high: 5 Å / D res low: 45 Å
Phasing MIRResolution: 5→45 Å / FOM: 0.42 / Reflection: 21767
Phasing MIR der
IDResolution (Å)Der set-IDNative set-ID
15-4511
21
31
41
51
61
Phasing MIR der site

Biso : 60 Å

IDDer-IDAtom type symbolFract xFract yFract zOccupancy
11Pt0.61940.82720.10242.3125
12Pt0.99250.6510.02471.4993
13Pt0.94480.71750.05221.6932
14Pt0.56430.8740.07421.2437
15Pt0.97950.49110.02320.7812
21Ir0.06910.57670.07230.8029
22Ir0.98130.5870.11130.7171
23Ir0.6530.92270.1060.4492
24Ir0.08970.53930.05660.1981
25Ir0.89980.63010.04320.4691
26Ir0.06760.82890.08030.2091
31Hg0.88560.73610.02020.616
32Hg0.60670.6260.04210.5542
41W0.01810.83950.0940.5051
42W0.00330.83510.06050.2912
43W0.83790.54540.00030.2924
44W0.10930.82330.09540.3601
Phasing MIR shell
Resolution (Å)FOMReflection
17.3-450.581153
11.16-17.30.581866
8.8-11.160.592330
7.49-8.80.572695
6.63-7.490.563028
6.01-6.630.353315
5.54-6.010.233584
5.16-5.540.233796

-
Processing

Software
NameVersionClassificationNB
PHASERphasing
SOLVE2.09phasing
PDB_EXTRACT1.701data extraction
Blu-Icedata collection
DENZOdata reduction
SCALEPACKdata scaling
CCP4(SCALA)data scaling
RefinementMethod to determine structure: molecular replacement, MIRAS / Resolution: 5→36 Å / Num. reflection obs: 21931
Details: No refinement done. The molecular replacement model contains Fc and the C-terminal domain of the HSV-1 gE ectodomain. HSV-1 gI ectodomain and the N-terminal domain of the HSV-1 gE ectodomain ...Details: No refinement done. The molecular replacement model contains Fc and the C-terminal domain of the HSV-1 gE ectodomain. HSV-1 gI ectodomain and the N-terminal domain of the HSV-1 gE ectodomain are contained in the crystal but not modeled in the structure.
Refinement stepCycle: LAST / Resolution: 5→36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5956 0 192 0 6148

+
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