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- PDB-1jma: CRYSTAL STRUCTURE OF THE HERPES SIMPLEX VIRUS GLYCOPROTEIN D BOUN... -

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Basic information

Entry
Database: PDB / ID: 1jma
TitleCRYSTAL STRUCTURE OF THE HERPES SIMPLEX VIRUS GLYCOPROTEIN D BOUND TO THE CELLULAR RECEPTOR HVEA/HVEM
Components
  • GLYCOPROTEIN D
  • HERPESVIRUS ENTRY MEDIATOR
KeywordsVIRAL PROTEIN / V-type Ig molecule and TNFR superfamily
Function / homology
Function and homology information


negative regulation of adaptive immune memory response / negative regulation of alpha-beta T cell proliferation / tumor necrosis factor receptor activity / TNFs bind their physiological receptors / positive regulation of cytokine production involved in immune response / Co-inhibition by BTLA / cytokine binding / positive regulation of T cell migration / negative regulation of T cell proliferation / T cell costimulation ...negative regulation of adaptive immune memory response / negative regulation of alpha-beta T cell proliferation / tumor necrosis factor receptor activity / TNFs bind their physiological receptors / positive regulation of cytokine production involved in immune response / Co-inhibition by BTLA / cytokine binding / positive regulation of T cell migration / negative regulation of T cell proliferation / T cell costimulation / virus receptor activity / defense response to Gram-negative bacterium / host cell Golgi apparatus / adaptive immune response / entry receptor-mediated virion attachment to host cell / cell surface receptor signaling pathway / defense response to Gram-positive bacterium / immune response / receptor ligand activity / innate immune response / external side of plasma membrane / viral envelope / ubiquitin protein ligase binding / symbiont entry into host cell / virion membrane / metal ion binding / membrane / plasma membrane
Similarity search - Function
Tumour necrosis factor receptor 14 / Tumor necrosis factor receptor 14/UL144, N-terminal / Glycoprotein D; Chain: A; / Glycoprotein D; Chain: A; - #10 / Herpesvirus glycoprotein D/GG/GX domain / Herpesvirus glycoprotein D/GG/GX domain / Tumor Necrosis Factor Receptor, subunit A, domain 2 / Tumor Necrosis Factor Receptor, subunit A; domain 2 / TNFR/NGFR family cysteine-rich region domain profile. / TNFR/NGFR cysteine-rich region ...Tumour necrosis factor receptor 14 / Tumor necrosis factor receptor 14/UL144, N-terminal / Glycoprotein D; Chain: A; / Glycoprotein D; Chain: A; - #10 / Herpesvirus glycoprotein D/GG/GX domain / Herpesvirus glycoprotein D/GG/GX domain / Tumor Necrosis Factor Receptor, subunit A, domain 2 / Tumor Necrosis Factor Receptor, subunit A; domain 2 / TNFR/NGFR family cysteine-rich region domain profile. / TNFR/NGFR cysteine-rich region / TNFR/NGFR family cysteine-rich region signature. / Tumor necrosis factor receptor / nerve growth factor receptor repeats. / TNFR/NGFR cysteine-rich region / Distorted Sandwich / Ribbon / Immunoglobulin-like domain superfamily / Mainly Beta
Similarity search - Domain/homology
Envelope glycoprotein D / Tumor necrosis factor receptor superfamily member 14
Similarity search - Component
Biological speciesHuman herpesvirus 1 (Herpes simplex virus type 1)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.65 Å
AuthorsCarfi, A. / Willis, S.H. / Whitbeck, J.C. / Krummenacker, C. / Cohen, G.H. / Eisenberg, R.J. / Wiley, D.C.
Citation
Journal: Mol.Cell / Year: 2001
Title: Herpes simplex virus glycoprotein D bound to the human receptor HveA.
Authors: Carfi, A. / Willis, S.H. / Whitbeck, J.C. / Krummenacher, C. / Cohen, G.H. / Eisenberg, R.J. / Wiley, D.C.
#1: Journal: Cell(Cambridge,Mass.) / Year: 1996
Title: Herpes simplex virus-1 entry into cells mediated by a novel member of the TNF/NGF receptor family
Authors: Montgomery, R.I. / Warner, M.S. / Lurn, B.J. / Spear, P.G.
History
DepositionJul 17, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 26, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...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 / struct_asym / struct_conn / 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.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 11Residues 1 to 3, 93,94 and 106 to 167 including 5 C-terminus HIS tag residues in chain B, and ...Residues 1 to 3, 93,94 and 106 to 167 including 5 C-terminus HIS tag residues in chain B, and residues 260 to 290 that includes 5 C-terimus HIS tag residues were not visible in the electron density maps due to disorder
Remark 12Weak or no electron density was observed for the side chains of the following residues: Chain B ...Weak or no electron density was observed for the side chains of the following residues: Chain B residues: 5, 6, 18, 31, 71, 95 and 96. Chain A residues: 16, 18, 20, 21, 35, 89, 91, 186, 196 and 259

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: HERPESVIRUS ENTRY MEDIATOR
A: GLYCOPROTEIN D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,9888
Polymers50,0842
Non-polymers9056
Water88349
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)129.154, 129.154, 80.940
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein HERPESVIRUS ENTRY MEDIATOR


Mass: 17767.955 Da / Num. of mol.: 1 / Fragment: HVEA-162 / Mutation: ECTODOMAIN OF THE FULL PROTEIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human herpesvirus 1 (Herpes simplex virus type 1)
Genus: Simplexvirus / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q92956
#2: Protein GLYCOPROTEIN D


Mass: 32315.697 Da / Num. of mol.: 1 / Fragment: GD-285 / Mutation: C-TERMINAL TRUNCATION AT RESIDUE 285
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P57083
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / Source method: isolated from a natural source / Formula: H2O
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: 3.89 Å3/Da / Density % sol: 68.36 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 1.8M Ammonium Sulfate and 5% Peg400 and Tris-HCL 100mM pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal grow
*PLUS
pH: 8 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
150 mMTris-HCl11
21.8 Mammonium sulfate11
35 %PEG40011

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.9196 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 19, 2000 / Details: monochromator
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9196 Å / Relative weight: 1
ReflectionResolution: 2.65→25 Å / Num. all: 24279 / Num. obs: 24260 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5 % / Biso Wilson estimate: 57 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 11
Reflection shellResolution: 2.65→20 Å / Rmerge(I) obs: 0.346 / Mean I/σ(I) obs: 5 / % possible all: 99.7
Reflection
*PLUS
Lowest resolution: 25 Å / Num. measured all: 272205
Reflection shell
*PLUS
% possible obs: 99.9 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
TRUNCATEdata reduction
CNSrefinement
CCP4(TRUNCATE)data scaling
CNSphasing
RefinementMethod to determine structure: MIRAS / Resolution: 2.65→20 Å / σ(F): 1 / Stereochemistry target values: Engh & Huber / Details: mlf refinement with CNS
RfactorNum. reflection% reflectionSelection details
Rfree0.259 1094 5 %random
Rwork0.236 ---
all0.237 22902 --
obs0.237 22562 99.7 %-
Displacement parametersBiso mean: 16.177 Å2
Baniso -1Baniso -2Baniso -3
1--11.423 Å2-11.044 Å20 Å2
2---11.423 Å222.846 Å2
3---0 Å2
Refine analyzeLuzzati sigma a obs: 0.35 Å
Refinement stepCycle: LAST / Resolution: 2.65→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2765 0 53 49 2867
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.54616
X-RAY DIFFRACTIONc_bond_d0.008
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / σ(F): 1 / % reflection Rfree: 5 % / Rfactor obs: 0.236
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_bond_d / Dev ideal: 0.008

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