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- PDB-2gj7: Crystal Structure of a gE-gI/Fc complex -

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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 / 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 / host cell Golgi membrane ...host cell junction / 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 / host cell Golgi membrane / FCGR activation / complement activation, classical pathway / Role of phospholipids in phagocytosis / antigen binding / FCGR3A-mediated IL10 synthesis / host cell endosome membrane / Regulation of Complement cascade / B cell receptor signaling pathway / FCGR3A-mediated phagocytosis / Regulation of actin dynamics for phagocytic cup formation / antibacterial humoral response / blood microparticle / Interleukin-4 and Interleukin-13 signaling / adaptive immune response / viral envelope / virion membrane / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / 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 ...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
Revision 2.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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
Water00
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).

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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
Has protein modificationY

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Experimental details

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Experiment

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

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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

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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

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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

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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

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