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- PDB-4fhq: Crystal Structure of HVEM -

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Basic information

Entry
Database: PDB / ID: 4fhq
TitleCrystal Structure of HVEM
ComponentsTumor necrosis factor receptor superfamily member 14
KeywordsIMMUNE SYSTEM / CYSTEINE RICH DOMAIN / TNF RECEPTOR / Structural Genomics / PSI-Biology / Protein Structure Initiative / Atoms-to-Animals: The Immune Function Network / IFN / TNFRSF / Cysteine Rich Domains / Receptor / TNF14 / BTLA / CD160 / gD of HSV / Membrane / New York Structural Genomics Research Consortium (NYSGRC)
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 / positive regulation of cytokine production involved in immune response / TNFs bind their physiological receptors / Costimulation by the CD28 family / cytokine binding / positive regulation of T cell migration / T cell costimulation / positive regulation of peptidyl-tyrosine phosphorylation ...negative regulation of adaptive immune memory response / negative regulation of alpha-beta T cell proliferation / tumor necrosis factor receptor activity / positive regulation of cytokine production involved in immune response / TNFs bind their physiological receptors / Costimulation by the CD28 family / cytokine binding / positive regulation of T cell migration / T cell costimulation / positive regulation of peptidyl-tyrosine phosphorylation / virus receptor activity / adaptive immune response / defense response to Gram-negative bacterium / cell surface receptor signaling pathway / defense response to Gram-positive bacterium / immune response / external side of plasma membrane / innate immune response / ubiquitin protein ligase binding / plasma membrane
Similarity search - Function
Tumour necrosis factor receptor 14 / Tumor necrosis factor receptor 14/UL144, N-terminal / 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 / Ribbon / Mainly Beta
Similarity search - Domain/homology
Tumor necrosis factor receptor superfamily member 14
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.251 Å
AuthorsLiu, W. / Zhan, C. / Patskovsky, Y. / Bhosle, R.C. / Nathenson, S.G. / Almo, S.C. / Atoms-to-Animals: The Immune Function Network (IFN) / New York Structural Genomics Research Consortium (NYSGRC)
CitationJournal: Mol Biotechnol / Year: 2015
Title: Increased Heterologous Protein Expression in Drosophila S2 Cells for Massive Production of Immune Ligands/Receptors and Structural Analysis of Human HVEM.
Authors: Liu, W. / Vigdorovich, V. / Zhan, C. / Patskovsky, Y. / Bonanno, J.B. / Nathenson, S.G. / Almo, S.C.
History
DepositionJun 6, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 18, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 25, 2012Group: Structure summary
Revision 1.2Sep 2, 2015Group: Database references
Revision 1.3Sep 16, 2015Group: Database references
Revision 1.4Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tumor necrosis factor receptor superfamily member 14


Theoretical massNumber of molelcules
Total (without water)14,3321
Polymers14,3321
Non-polymers00
Water362
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)94.736, 94.736, 77.159
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
DetailsAUTHOR DETERMINED BIOLOGICAL UNIT: NOT DETERMINED

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Components

#1: Protein Tumor necrosis factor receptor superfamily member 14 / Herpes virus entry mediator A / Herpesvirus entry mediator A / HveA / Tumor necrosis factor ...Herpes virus entry mediator A / Herpesvirus entry mediator A / HveA / Tumor necrosis factor receptor-like 2 / TR2


Mass: 14332.176 Da / Num. of mol.: 1 / Fragment: extracellular domain residues 39-162
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HVEA, HVEM, TNFRSF14, UNQ329/PRO509 / Plasmid: pMT-Bip-His / Cell (production host): Schneider 2 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: Q92956
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O

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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 Å3/Da / Density % sol: 58.99 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M SODIUM ACETATE TRIHYDRATE, PH 8.5, TRIS-HCL, 30% W/V PEG4000, VAPOR DIFFUSION, SITTING DROP, temperature 294.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 15, 2012 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. obs: 8551 / % possible obs: 99.3 % / Redundancy: 7.6 % / Biso Wilson estimate: 54.17 Å2 / Rmerge(I) obs: 0.104 / Rsym value: 0.09 / Net I/σ(I): 16.68
Reflection shellResolution: 2.25→2.29 Å / Redundancy: 6.4 % / Mean I/σ(I) obs: 1.062 / % possible all: 94.7

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Processing

Software
NameVersionClassification
CBASSdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2AW2

2aw2


Resolution: 2.251→33.494 Å / SU ML: 0.47 / σ(F): 0 / Phase error: 38.13 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2925 252 2.95 %random
Rwork0.2792 ---
obs0.2796 8548 99.11 %-
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 66.537 Å2 / ksol: 0.359 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--8.1744 Å2-0 Å20 Å2
2---8.1744 Å20 Å2
3---16.3488 Å2
Refinement stepCycle: LAST / Resolution: 2.251→33.494 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms733 0 0 2 735
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006756
X-RAY DIFFRACTIONf_angle_d1.0571011
X-RAY DIFFRACTIONf_dihedral_angle_d15.506280
X-RAY DIFFRACTIONf_chiral_restr0.064107
X-RAY DIFFRACTIONf_plane_restr0.004137
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2511-2.83590.42521280.37864029X-RAY DIFFRACTION98
2.8359-33.49790.26121240.25834267X-RAY DIFFRACTION100
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)
15.28462.2781-0.61812.9370.64380.4666-0.57871.13690.43510.11690.078-0.2568-0.0885-0.0550.30080.5071-0.1899-0.14210.64260.34590.824-22.701731.97059.5934
23.6517-0.90622.24364.6096-3.25034.44270.04630.89150.4248-0.17080.3873-0.57420.43750.1134-0.18980.47350.067-0.55040.47680.10211.17431.701929.170620.7558
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 1:84)
2X-RAY DIFFRACTION2chain 'A' and (resseq 85:103)

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