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- PDB-5t2q: Unliganded Human HVEM at 1.9A in P 1 21 1 -

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Basic information

Entry
Database: PDB / ID: 5t2q
TitleUnliganded Human HVEM at 1.9A in P 1 21 1
ComponentsTumor necrosis factor receptor superfamily member 14
KeywordsIMMUNE SYSTEM / human HVEM / unliganded / herpesvirus entry mediator
Function / homology
Function and homology information


regulation of T cell tolerance induction to tumor cell / negative regulation of adaptive immune memory response / negative regulation of alpha-beta T cell proliferation / regulation of B cell proliferation / negative regulation of T cell cytokine production / tumor necrosis factor receptor activity / immune response-regulating cell surface receptor signaling pathway / TNFs bind their physiological receptors / regulation of type II interferon production / positive regulation of cytokine production involved in immune response ...regulation of T cell tolerance induction to tumor cell / negative regulation of adaptive immune memory response / negative regulation of alpha-beta T cell proliferation / regulation of B cell proliferation / negative regulation of T cell cytokine production / tumor necrosis factor receptor activity / immune response-regulating cell surface receptor signaling pathway / TNFs bind their physiological receptors / regulation of type II interferon production / positive regulation of cytokine production involved in immune response / Co-inhibition by BTLA / T cell proliferation / negative regulation of T cell activation / cytokine binding / negative regulation of T cell proliferation / regulation of ERK1 and ERK2 cascade / T cell costimulation / positive regulation of T cell migration / virus receptor activity / defense response to Gram-negative bacterium / adaptive immune response / cell surface receptor signaling pathway / defense response to Gram-positive bacterium / immune response / receptor ligand activity / 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: 1.9 Å
AuthorsNemcovicova, I. / Zajonc, D.M.
Funding support Slovakia, 3items
OrganizationGrant numberCountry
Slovak Research and Development AgencyAPVV-14-0839 Slovakia
Scientific Grant Agency of the Slovak Republic2/0103/15 Slovakia
Marie Curie ActionSASPRO-0003/01/02 Slovakia
CitationJournal: To Be Published
Title: Unliganded Human HVEM at 1.9A in P 1 21 1
Authors: Nemcovicova, I. / Zajonc, D.M.
History
DepositionAug 24, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Oct 24, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 6, 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: Tumor necrosis factor receptor superfamily member 14
B: Tumor necrosis factor receptor superfamily member 14


Theoretical massNumber of molelcules
Total (without water)22,9022
Polymers22,9022
Non-polymers00
Water1,67593
1
A: Tumor necrosis factor receptor superfamily member 14


Theoretical massNumber of molelcules
Total (without water)11,4511
Polymers11,4511
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Tumor necrosis factor receptor superfamily member 14


Theoretical massNumber of molelcules
Total (without water)11,4511
Polymers11,4511
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.190, 47.510, 67.290
Angle α, β, γ (deg.)90.00, 106.69, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 11451.132 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNFRSF14, HVEA, HVEM, UNQ329/PRO509 / Plasmid: pAc / Details (production host): GP secretion signal / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q92956
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / 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: 3.36 Å3/Da / Density % sol: 63.34 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop
Details: 0.15 M CaCl2, 15% (w/v) PEG 3300, 30% (w/v) PEG 8K, 5% (v/v) Glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.975 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 16, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.975 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. obs: 23026 / % possible obs: 99.25 % / Redundancy: 7.6 % / Rmerge(I) obs: 0.105 / Rsym value: 0.087 / Net I/σ(I): 16.2
Reflection shellResolution: 1.9→1.98 Å / Redundancy: 6.4 % / Mean I/σ(I) obs: 1.062 / % possible all: 94.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0151refinement
iMOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2AW2

2aw2


Resolution: 1.9→20 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.93 / SU B: 7.085 / SU ML: 0.177 / Cross valid method: THROUGHOUT / ESU R: 0.15 / ESU R Free: 0.145
RfactorNum. reflection% reflectionSelection details
Rfree0.28751 957 4 %RANDOM
Rwork0.25226 ---
obs0.25373 23026 99.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso mean: 46.689 Å2
Baniso -1Baniso -2Baniso -3
1--0.14 Å20 Å2-0.41 Å2
2---0.19 Å2-0 Å2
3---0.49 Å2
Refinement stepCycle: 1 / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1488 0 0 93 1581
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0191535
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0621.9812088
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.1485203
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.00624.06859
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.71215239
X-RAY DIFFRACTIONr_dihedral_angle_4_deg27.7311510
X-RAY DIFFRACTIONr_chiral_restr0.1470.2219
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0221176
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.6854.178818
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it6.4417.7931019
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it6.8875.002717
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined11.61462.3462155
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å
RfactorNum. reflection% reflection
Rfree0.287 69 -
Rwork0.253 1621 -
obs--97.07 %

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