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- PDB-6nyp: Crystal structure of UL144/BTLA complex -

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Basic information

Entry
Database: PDB / ID: 6nyp
TitleCrystal structure of UL144/BTLA complex
Components
  • B- and T-lymphocyte attenuator
  • UL144
KeywordsIMMUNE SYSTEM/VIRAL PROTEIN / Immune evasion protein / VIRAL PROTEIN / IMMUNE SYSTEM-VIRAL PROTEIN complex
Function / homology
Function and homology information


immune response-regulating cell surface receptor signaling pathway / Costimulation by the CD28 family / signaling receptor activity / adaptive immune response / plasma membrane
Similarity search - Function
B- and T-lymphocyte attenuator / Immunoglobulin / Immunoglobulin domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold ...B- and T-lymphocyte attenuator / Immunoglobulin / Immunoglobulin domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
B- and T-lymphocyte attenuator
Similarity search - Component
Biological speciesHomo sapiens (human)
Macacine herpesvirus 1 (monkey B virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å
AuthorsAruna, B. / Zajonc, D.M. / Doukov, T.
CitationJournal: J.Biol.Chem. / Year: 2019
Title: Structure of human cytomegalovirus UL144, an HVEM orthologue, bound to the B and T cell lymphocyte attenuator.
Authors: Bitra, A. / Nemcovicova, I. / Picarda, G. / Doukov, T. / Wang, J. / Benedict, C.A. / Zajonc, D.M.
History
DepositionFeb 11, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jul 17, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_conn_type / 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.conn_type_id / _struct_conn.id / _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_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: B- and T-lymphocyte attenuator
B: B- and T-lymphocyte attenuator
C: B- and T-lymphocyte attenuator
D: B- and T-lymphocyte attenuator
E: UL144
F: UL144
G: UL144
H: UL144
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,35518
Polymers102,2958
Non-polymers1,06110
Water1,00956
1
A: B- and T-lymphocyte attenuator
F: UL144
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0066
Polymers25,5742
Non-polymers4324
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2290 Å2
ΔGint-28 kcal/mol
Surface area10620 Å2
MethodPISA
2
B: B- and T-lymphocyte attenuator
H: UL144
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7953
Polymers25,5742
Non-polymers2211
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1930 Å2
ΔGint-1 kcal/mol
Surface area10560 Å2
MethodPISA
3
C: B- and T-lymphocyte attenuator
G: UL144
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7664
Polymers25,5742
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2330 Å2
ΔGint-36 kcal/mol
Surface area10400 Å2
MethodPISA
4
D: B- and T-lymphocyte attenuator
E: UL144
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7895
Polymers25,5742
Non-polymers2153
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2280 Å2
ΔGint-44 kcal/mol
Surface area9530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.990, 77.200, 101.720
Angle α, β, γ (deg.)90.000, 91.670, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D
17E
27F
18E
28G
19E
29H
110F
210G
111F
211H
112G
212H

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A35 - 134
2010B35 - 134
1020A34 - 134
2020C34 - 134
1030A34 - 134
2030D34 - 134
1040B35 - 134
2040C35 - 134
1050B35 - 134
2050D35 - 134
1060C34 - 134
2060D34 - 134
1070E22 - 91
2070F22 - 81
1080E22 - 91
2080G22 - 84
1090E22 - 91
2090H22 - 81
10100F22 - 93
20100G22 - 93
10110F22 - 98
20110H22 - 98
10120G22 - 93
20120H22 - 93

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12

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Components

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Protein , 2 types, 8 molecules ABCDEFGH

#1: Protein
B- and T-lymphocyte attenuator / B- and T-lymphocyte-associated protein


Mass: 12387.949 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BTLA / Production host: Escherichia coli (E. coli) / References: UniProt: Q7Z6A9
#2: Protein
UL144


Mass: 13185.677 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macacine herpesvirus 1 (monkey B virus)
Production host: Spodoptera frugiperda (fall armyworm)

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Sugars , 1 types, 2 molecules

#6: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: isolated from a natural 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 , 4 types, 64 molecules

#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C3H8O3
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 2.61 Å3/Da / Density % sol: 52.84 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / Details: 0.1 M CHES pH 9.5, 20 % W/V PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 2.0663 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jan 31, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 2.0663 Å / Relative weight: 1
ReflectionResolution: 2.7→39.93 Å / Num. obs: 28639 / % possible obs: 99.5 % / Redundancy: 53.66 % / Biso Wilson estimate: 75.15 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.163 / Rrim(I) all: 0.164 / Χ2: 1.071 / Net I/σ(I): 26.91
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.7-2.7753.343.8531.4540850.6153.88997.9
2.77-2.8552.7182.9211.9839880.7572.94999
2.85-2.9351.0762.0842.8238810.8582.10498.8
2.93-3.0251.5311.4743.9737870.9221.48899.1
3.02-3.1253.1331.0055.9436600.961.01599.5
3.12-3.2355.020.728.2935770.9770.72799.6
3.23-3.3554.8580.4911.9934580.9890.49499.9
3.35-3.4953.2520.37215.8432800.9930.37599.4
3.49-3.6451.3380.26320.4131960.9970.265100
3.64-3.8251.8330.21125.5129990.9970.21399.9
3.82-4.0355.2910.15134.5728900.9990.15299.7
4.03-4.2756.4870.10149.3427600.9990.101100
4.27-4.5655.5940.08158.3255210.082100
4.56-4.9353.0650.07759.8240210.078100
4.93-5.450.8340.07459.16217810.075100
5.4-6.0457.9650.0858.81202010.081100
6.04-6.9758.130.07961.96172910.07999.8
6.97-8.5454.9620.0675.8150810.061100
8.54-12.0852.2530.04493.12112110.045100
12.08-39.9359.6130.043114.7660810.04497

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XSCALEdata scaling
PDB_EXTRACT3.24data extraction
BUCCANEERmodel building
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: SAD / Resolution: 2.7→39.93 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.908 / SU B: 13.337 / SU ML: 0.264 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.652 / ESU R Free: 0.342
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2765 1432 5 %RANDOM
Rwork0.2297 ---
obs0.232 27207 99.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 180.01 Å2 / Biso mean: 73.28 Å2 / Biso min: 30 Å2
Baniso -1Baniso -2Baniso -3
1--0.38 Å20 Å20.4 Å2
2---0.3 Å20 Å2
3---0.65 Å2
Refinement stepCycle: final / Resolution: 2.7→39.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5391 0 61 56 5508
Biso mean--112.72 64.85 -
Num. residues----696
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0135586
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174752
X-RAY DIFFRACTIONr_angle_refined_deg1.3551.6697624
X-RAY DIFFRACTIONr_angle_other_deg1.1391.57711158
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.4185684
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.91723.978269
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.10715898
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8471522
X-RAY DIFFRACTIONr_chiral_restr0.0510.2778
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.026142
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021060
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A28730.1
12B28730.1
21A28010.12
22C28010.12
31A28420.13
32D28420.13
41B27540.13
42C27540.13
51B27830.14
52D27830.14
61C28950.11
62D28950.11
71E14290.15
72F14290.15
81E13890.14
82G13890.14
91E14010.16
92H14010.16
101F16670.16
102G16670.16
111F19980.1
112H19980.1
121G16570.15
122H16570.15
LS refinement shellResolution: 2.7→2.77 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.378 104 -
Rwork0.355 1974 -
all-2078 -
obs--98.53 %

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