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- PDB-5t2r: Unliganded Human HVEM at 2.1A in P 21 21 21 -

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Basic information

Entry
Database: PDB / ID: 5t2r
TitleUnliganded Human HVEM at 2.1A in P 21 21 21
ComponentsTumor necrosis factor receptor superfamily member 14
KeywordsIMMUNE SYSTEM / herpesvirus entry mediator / HVEM / TNFRSF14
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: 2.1 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 Republic02/0103/15 Slovakia
Marie Curie ActionSASPRO 0003/01/02 Slovakia
CitationJournal: To Be Published
Title: Unliganded Human HVEM at 2.1A in P 21 21 21
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

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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
Water93752
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)47.210, 62.420, 103.570
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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 / Details (production host): GP secretion signal / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q92956
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 3.33 Å3/Da / Density % sol: 63.08 %
Crystal growTemperature: 296.15 K / Method: vapor diffusion, sitting drop
Details: 0.15 M HEPES 7.5, 0.15 M NaCl, 0.05 M AS, 30% (w/v) PEG 8K, 5% (v/v) Glycerol
Temp details: RT

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.978 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 16, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. obs: 17307 / % possible obs: 98.8 % / Redundancy: 7.6 % / Rmerge(I) obs: 0.111 / Rsym value: 0.103 / Net I/σ(I): 16
Reflection shellResolution: 2.1→2.16 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 2.7 / % possible all: 94.2

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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: 2.1→20 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.906 / SU B: 9.14 / SU ML: 0.214 / Cross valid method: THROUGHOUT / ESU R: 0.221 / ESU R Free: 0.207
RfactorNum. reflection% reflectionSelection details
Rfree0.32144 984 5.4 %RANDOM
Rwork0.27463 ---
obs0.27712 17307 98.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso mean: 48.375 Å2
Baniso -1Baniso -2Baniso -3
1-0.4 Å20 Å20 Å2
2--0.18 Å2-0 Å2
3----0.58 Å2
Refinement stepCycle: 1 / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1505 0 0 52 1557
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0191553
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0031.9772111
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.7335205
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.5772460
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.58815241
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6761510
X-RAY DIFFRACTIONr_chiral_restr0.1150.2220
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0221188
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_it4.2744.363826
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it6.1758.1491029
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it7.2715.213727
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined13.79264.0192088
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: 2.1→2.154 Å
RfactorNum. reflection% reflection
Rfree0.45 71 -
Rwork0.45 1257 -
obs--98.15 %

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