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- PDB-4rsu: Crystal structure of the light and hvem complex -

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Basic information

Entry
Database: PDB / ID: 4rsu
TitleCrystal structure of the light and hvem complex
Components(Tumor necrosis factor ...) x 2
KeywordsIMMUNE SYSTEM / STRUCTURAL GENOMICS / PSI-BIOLOGY / NEW YORK STRUCTURAL GENOMICS / RESEARCH CONSORTIUM / NYSGRC / IMMUNITY / N-GLYCOSYLATION / MEMBRANE / SECRETED PROTEIN / CYTOKINE / IFN / JELLY-ROLL FOLD / Protein Structure Initiative / Atoms-to-Animals: The Immune Function Network / cysteine rich domain / signaling / cell membrane / secreted / New York Structural Genomics Research Consortium
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 / TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway / positive regulation of T cell chemotaxis / T cell chemotaxis / tumor necrosis factor receptor binding / Costimulation by the CD28 family ...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 / TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway / positive regulation of T cell chemotaxis / T cell chemotaxis / tumor necrosis factor receptor binding / Costimulation by the CD28 family / positive regulation of myoblast fusion / cytokine binding / T cell homeostasis / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / positive regulation of T cell migration / positive regulation of myoblast differentiation / T cell proliferation / T cell costimulation / T cell activation / cytokine activity / TNFR2 non-canonical NF-kB pathway / cellular response to mechanical stimulus / positive regulation of non-canonical NF-kappaB signal transduction / positive regulation of peptidyl-tyrosine phosphorylation / 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 / external side of plasma membrane / signaling receptor binding / innate immune response / apoptotic process / ubiquitin protein ligase binding / signal transduction / extracellular space / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
Tumour necrosis factor receptor 14 / Tumor necrosis factor receptor 14/UL144, N-terminal / Tumour necrosis factor / Tumor Necrosis Factor Receptor, subunit A, domain 2 / Tumor Necrosis Factor Receptor, subunit A; domain 2 / Tumour necrosis factor family. / TNF family profile. / TNF(Tumour Necrosis Factor) family / Tumour necrosis factor domain / TNFR/NGFR family cysteine-rich region domain profile. ...Tumour necrosis factor receptor 14 / Tumor necrosis factor receptor 14/UL144, N-terminal / Tumour necrosis factor / Tumor Necrosis Factor Receptor, subunit A, domain 2 / Tumor Necrosis Factor Receptor, subunit A; domain 2 / Tumour necrosis factor family. / TNF family profile. / TNF(Tumour Necrosis Factor) family / Tumour necrosis factor domain / 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 / Jelly Rolls - #40 / Tumour necrosis factor-like domain superfamily / Ribbon / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Tumor necrosis factor ligand superfamily member 14 / Tumor necrosis factor receptor superfamily member 14
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsLiu, W. / Ramagoal, U.A. / Himmel, D. / Bonanno, J.B. / Nathenson, S.G. / Almo, S.C. / Atoms-to-Animals: The Immune Function Network (IFN) / New York Structural Genomics Research Consortium (NYSGRC)
CitationJournal: J.Exp.Med. / Year: 2021
Title: HVEM structures and mutants reveal distinct functions of binding to LIGHT and BTLA/CD160.
Authors: Liu, W. / Chou, T.F. / Garrett-Thomson, S.C. / Seo, G.Y. / Fedorov, E. / Ramagopal, U.A. / Bonanno, J.B. / Wang, Q. / Kim, K. / Garforth, S.J. / Kakugawa, K. / Cheroutre, H. / Kronenberg, M. / Almo, S.C.
History
DepositionNov 11, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 4, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 11, 2015Group: Structure summary
Revision 1.2Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Apr 27, 2022Group: Database references / Structure summary
Category: chem_comp / citation ...chem_comp / citation / citation_author / database_2
Item: _chem_comp.pdbx_synonyms / _citation.country ..._chem_comp.pdbx_synonyms / _citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tumor necrosis factor ligand superfamily member 14, soluble form
B: Tumor necrosis factor ligand superfamily member 14, soluble form
C: Tumor necrosis factor ligand superfamily member 14, soluble form
D: Tumor necrosis factor receptor superfamily member 14
E: Tumor necrosis factor receptor superfamily member 14
F: Tumor necrosis factor receptor superfamily member 14
G: Tumor necrosis factor ligand superfamily member 14, soluble form
H: Tumor necrosis factor ligand superfamily member 14, soluble form
I: Tumor necrosis factor ligand superfamily member 14, soluble form
J: Tumor necrosis factor receptor superfamily member 14
K: Tumor necrosis factor receptor superfamily member 14
L: Tumor necrosis factor receptor superfamily member 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)197,46339
Polymers195,12412
Non-polymers2,33927
Water4,017223
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area34450 Å2
ΔGint-283 kcal/mol
Surface area60660 Å2
MethodPISA
2
A: Tumor necrosis factor ligand superfamily member 14, soluble form
B: Tumor necrosis factor ligand superfamily member 14, soluble form
C: Tumor necrosis factor ligand superfamily member 14, soluble form
D: Tumor necrosis factor receptor superfamily member 14
E: Tumor necrosis factor receptor superfamily member 14
F: Tumor necrosis factor receptor superfamily member 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,62119
Polymers97,5626
Non-polymers1,05913
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15110 Å2
ΔGint-136 kcal/mol
Surface area31480 Å2
MethodPISA
3
G: Tumor necrosis factor ligand superfamily member 14, soluble form
H: Tumor necrosis factor ligand superfamily member 14, soluble form
I: Tumor necrosis factor ligand superfamily member 14, soluble form
J: Tumor necrosis factor receptor superfamily member 14
K: Tumor necrosis factor receptor superfamily member 14
L: Tumor necrosis factor receptor superfamily member 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,84220
Polymers97,5626
Non-polymers1,28014
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16080 Å2
ΔGint-131 kcal/mol
Surface area32440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.651, 113.604, 163.279
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsA LIGHT trimer binds to three HVEM.

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Components

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Tumor necrosis factor ... , 2 types, 12 molecules ABCGHIDEFJKL

#1: Protein
Tumor necrosis factor ligand superfamily member 14, soluble form / Herpes virus entry mediator ligand / HVEM-L / Herpesvirus entry mediator ligand / Tumor necrosis ...Herpes virus entry mediator ligand / HVEM-L / Herpesvirus entry mediator ligand / Tumor necrosis factor ligand superfamily member 14


Mass: 18188.549 Da / Num. of mol.: 6 / Fragment: EXTRACELLULAR DOMAIN, residues 83-240
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNFSF14, HVEML, LIGHT, UNQ391/PRO726 / Plasmid: pMT/Bip/His/V5 / Production host: Drosophila (fruit flies) / Strain (production host): S2 / References: UniProt: O43557
#2: 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.: 6 / Fragment: TNFR-Cys 1-3 repeats, residues 39-162
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNFRSF14, HVEA, HVEM, UNQ329/PRO509 / Plasmid: pMT/Bip/His/V5 / Production host: Drosophila (fruit flies) / Strain (production host): S2 / References: UniProt: Q92956

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Sugars , 1 types, 5 molecules

#5: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 245 molecules

#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 223 / 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: 2.65 Å3/Da / Density % sol: 53.65 %
Crystal growTemperature: 290 K / pH: 5.5
Details: 0.2M MAGNESIUM CHLORIDE, 0.1M BIS:TRIS BUFFER, 9% W/V PEG3350, PH 5.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 290.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 5, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 92792 / % possible obs: 99.9 % / Redundancy: 10.8 % / Rmerge(I) obs: 0.125 / Rsym value: 0.084 / Net I/σ(I): 21.7
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 10.7 % / Rmerge(I) obs: 0.936 / Mean I/σ(I) obs: 3.1 / Rsym value: 0.818 / % possible all: 99.7

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.8.0073refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4KG8, 4FHQ

4kg8

4fhq


Resolution: 2.3→48.92 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.927 / SU B: 13.035 / SU ML: 0.149 / Cross valid method: THROUGHOUT / ESU R: 0.232 / ESU R Free: 0.196 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23145 4631 5 %RANDOM
Rwork0.1883 ---
obs0.19052 87967 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.402 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å2-0 Å2-0 Å2
2---0.03 Å20 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 2.3→48.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11198 0 132 223 11553
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.01911616
X-RAY DIFFRACTIONr_bond_other_d0.0060.0210677
X-RAY DIFFRACTIONr_angle_refined_deg2.0811.98115775
X-RAY DIFFRACTIONr_angle_other_deg0.893324619
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8751477
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.56922.572451
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.347151776
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5341588
X-RAY DIFFRACTIONr_chiral_restr0.1070.21734
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02113084
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022584
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_it2.8383.1665965
X-RAY DIFFRACTIONr_mcbond_other2.8343.1655964
X-RAY DIFFRACTIONr_mcangle_it4.3834.7217423
X-RAY DIFFRACTIONr_mcangle_other4.1994.5697467
X-RAY DIFFRACTIONr_scbond_it3.7223.5275651
X-RAY DIFFRACTIONr_scbond_other3.5243.4145700
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.2994.9798423
X-RAY DIFFRACTIONr_long_range_B_refined7.43724.3612400
X-RAY DIFFRACTIONr_long_range_B_other7.43824.36612401
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 326 -
Rwork0.245 6367 -
obs--99.13 %
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)
10.35630.1638-0.08030.5786-0.04680.43450.0239-0.04150.00310.0299-0.00630.00130.01650.0198-0.01770.0096-0.01070.00360.0217-0.00230.012415.4023-12.7591111.0276
20.51940.08590.10330.61280.01140.3678-0.02790.10770.0033-0.0630.04490.0490.065-0.0199-0.0170.0321-0.0282-0.00340.0419-0.00210.00945.3781-19.454492.254
30.5864-0.10980.02410.3439-0.01920.64720.01660.0120.00970.00930.01180.06980.0497-0.1042-0.02850.0205-0.030.00130.05070.00770.0344-6.5103-17.8995111.176
40.6838-0.61360.29091.3027-0.39840.59950.03030.0598-0.0296-0.1132-0.0462-0.09440.07420.0590.01590.01680.00250.01670.0155-0.01260.032330.0956-15.195393.195
50.08660.15480.11441.11450.39660.688-0.02840.00980.0194-0.0363-0.01990.23490.0812-0.18770.04830.0539-0.0542-0.03390.10320.00940.0858-17.1717-24.933288.9984
60.42290.3103-0.25181.1149-0.49730.50880.0827-0.02870.00310.1026-0.04670.0282-0.0785-0.0303-0.0360.0555-0.02080.02340.0408-0.00640.0171.5684-14.0797132.5899
70.41370.0297-0.04850.42440.01310.41310.01340.0192-0.0176-0.00770.0011-0.01360.00460.0189-0.01450.0068-0.008-0.00330.0157-00.011338.735511.52594.3803
80.4385-0.03430.00910.50170.00770.35020.0447-0.0642-0.02740.0804-0.0318-0.0355-0.0240.0359-0.01290.0348-0.0229-0.0120.0377-0.00210.011145.621320.6877113.2646
90.3287-0.01910.04710.38570.02420.39460.00650.0150.06080.0012-0.00710.0014-0.11220.03040.00070.0449-0.02050.00440.0171-0.00290.029142.879433.308795.4562
100.8959-0.3789-0.28730.72640.22220.92450.0103-0.0985-0.07130.0437-0.0007-0.05190.14390.1077-0.00970.05340.0019-0.0180.02560.01670.027541.5592-4.5196110.8222
111.0917-0.18670.62050.4205-0.08360.6951-0.0203-0.08290.1370.0173-0.0169-0.0034-0.14830.01930.03730.1098-0.0381-0.00110.0385-0.03790.059852.297242.4627117.5627
122.41920.3807-0.94280.2335-0.21970.6094-0.04660.10270.0621-0.03020.0670.0209-0.0459-0.0342-0.02040.0294-0.02-0.00740.03320.01540.009535.628325.712574.3141
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A92 - 240
2X-RAY DIFFRACTION2B91 - 240
3X-RAY DIFFRACTION3C92 - 240
4X-RAY DIFFRACTION4D38 - 142
5X-RAY DIFFRACTION5E37 - 141
6X-RAY DIFFRACTION6F38 - 140
7X-RAY DIFFRACTION7G91 - 240
8X-RAY DIFFRACTION8H91 - 240
9X-RAY DIFFRACTION9I92 - 240
10X-RAY DIFFRACTION10J37 - 142
11X-RAY DIFFRACTION11K37 - 142
12X-RAY DIFFRACTION12L41 - 144

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