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- PDB-2aw2: Crystal structure of the human BTLA-HVEM complex -

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Basic information

Entry
Database: PDB / ID: 2aw2
TitleCrystal structure of the human BTLA-HVEM complex
Components
  • B and T lymphocyte attenuator
  • Tumor necrosis factor receptor superfamily member 14
KeywordsIMMUNE SYSTEM / IgI domain / IgG domain / TNFRSF / protein-protein complex
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 / immune response-regulating cell surface receptor signaling pathway / TNFs bind their physiological receptors / positive regulation of cytokine production involved in immune response / Co-inhibition by BTLA / cytokine binding / positive regulation of T cell migration / negative regulation of T cell proliferation ...negative regulation of adaptive immune memory response / negative regulation of alpha-beta T cell proliferation / tumor necrosis factor receptor activity / immune response-regulating cell surface receptor signaling pathway / TNFs bind their physiological receptors / positive regulation of cytokine production involved in immune response / Co-inhibition by BTLA / cytokine binding / positive regulation of T cell migration / negative regulation of T cell proliferation / T cell costimulation / signaling receptor activity / 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
B- and T-lymphocyte attenuator / 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 ...B- and T-lymphocyte attenuator / 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 / Immunoglobulin domain / Ribbon / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
NICKEL (II) ION / B- and T-lymphocyte attenuator / Tumor necrosis factor receptor superfamily member 14
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsCompaan, D.M. / Gonzalez, L.C. / Tom, I. / Loyet, K.M. / Eaton, D. / Hymowitz, S.G.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Attenuating Lymphocyte Activity: the crystal structure of the BTLA-HVEM complex
Authors: Compaan, D.M. / Gonzalez, L.C. / Tom, I. / Loyet, K.M. / Eaton, D. / Hymowitz, S.G.
History
DepositionAug 31, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 27, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _pdbx_struct_special_symmetry.label_asym_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_seq_id / _struct_conn.ptnr1_label_asym_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_conn.ptnr2_symmetry / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id
Revision 2.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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: Tumor necrosis factor receptor superfamily member 14
X: B and T lymphocyte attenuator
Y: Tumor necrosis factor receptor superfamily member 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,9567
Polymers51,1064
Non-polymers8503
Water724
1
A: B and T lymphocyte attenuator
B: Tumor necrosis factor receptor superfamily member 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0364
Polymers25,5532
Non-polymers4832
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
X: B and T lymphocyte attenuator
Y: Tumor necrosis factor receptor superfamily member 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9203
Polymers25,5532
Non-polymers3671
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2180 Å2
ΔGint2 kcal/mol
Surface area12470 Å2
MethodPISA
3
A: B and T lymphocyte attenuator
B: Tumor necrosis factor receptor superfamily member 14
hetero molecules

X: B and T lymphocyte attenuator
Y: Tumor necrosis factor receptor superfamily member 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,9567
Polymers51,1064
Non-polymers8503
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_545x+1/2,y-1/2,z1
Buried area5620 Å2
ΔGint-3 kcal/mol
Surface area23960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.294, 167.116, 148.680
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-1-

NI

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21X
12B
22Y

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11CYSCYSHISHIS6AA34 - 1409 - 115
21CYSCYSHISHIS6XC34 - 1409 - 115
12PROPROTYRTYR4BB2 - 1036 - 107
22PROPROTYRTYR4YD2 - 1036 - 107

NCS ensembles :
ID
1
2

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Components

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Protein , 2 types, 4 molecules AXBY

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


Mass: 14101.793 Da / Num. of mol.: 2 / Fragment: extracellular domain (residues 26-137)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BTLA / Plasmid: pSTII.TIR3 / Production host: Escherichia coli (E. coli) / Strain (production host): 33D3 / References: UniProt: Q7Z6A9
#2: Protein Tumor necrosis factor receptor superfamily member 14 / Herpesvirus entry mediator A / Tumor necrosis factor receptor-like 2 / TR2


Mass: 11451.132 Da / Num. of mol.: 2
Fragment: truncated extracellular domain contains CRD1, 2 and part of CRD3 (residues 39-142)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNFRSF14, HVEA, HVEM / Plasmid: pAcGP67-B / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Hi5 / References: UniProt: Q92956

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Sugars , 2 types, 2 molecules

#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#4: Polysaccharide beta-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpb1-6DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1b_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(6+1)][b-L-Fucp]{}}}LINUCSPDB-CARE

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Non-polymers , 2 types, 5 molecules

#5: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.3 Å3/Da / Density % sol: 62 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 2.0 M NaFormate, 0.1 M Na Acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 8, 2005
RadiationMonochromator: single crystal optically bent, Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. all: 15639 / Num. obs: 15639 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.98 % / Biso Wilson estimate: 70 Å2 / Rmerge(I) obs: 0.052 / Rsym value: 0.052 / Net I/σ(I): 13.4
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 4 % / Rmerge(I) obs: 0.455 / Mean I/σ(I) obs: 2.3 / Num. unique all: 1543 / Rsym value: 0.455 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1XAU and chain B from 1JMA

1xau

1jma


Resolution: 2.8→30 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.88 / SU B: 33.204 / SU ML: 0.3 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 / ESU R: 1.303 / ESU R Free: 0.392 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27838 1686 10.8 %Thin shells
Rwork0.23127 ---
all0.2364 15599 --
obs0.23649 15591 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 61.821 Å2
Baniso -1Baniso -2Baniso -3
1-2.72 Å20 Å20 Å2
2---1.88 Å20 Å2
3----0.83 Å2
Refinement stepCycle: LAST / Resolution: 2.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3202 0 53 4 3259
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0213358
X-RAY DIFFRACTIONr_bond_other_d0.0020.022841
X-RAY DIFFRACTIONr_angle_refined_deg1.0391.9624571
X-RAY DIFFRACTIONr_angle_other_deg0.6836659
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4745411
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.26724.014147
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.71515522
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.7841518
X-RAY DIFFRACTIONr_chiral_restr0.0610.2498
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.023685
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02641
X-RAY DIFFRACTIONr_nbd_refined0.1710.2531
X-RAY DIFFRACTIONr_nbd_other0.1640.22609
X-RAY DIFFRACTIONr_nbtor_refined0.1740.21490
X-RAY DIFFRACTIONr_nbtor_other0.080.22100
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1250.248
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1720.223
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2260.218
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0330.21
X-RAY DIFFRACTIONr_mcbond_it1.9092.52656
X-RAY DIFFRACTIONr_mcbond_other0.2832.5838
X-RAY DIFFRACTIONr_mcangle_it2.51853355
X-RAY DIFFRACTIONr_scbond_it1.5272.51467
X-RAY DIFFRACTIONr_scangle_it2.30851216
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
2B1366medium positional0.310.5
1A1554loose positional0.85
2B1366medium thermal0.232
1A1554loose thermal1.3410
LS refinement shellResolution: 2.8→2.857 Å / Total num. of bins used: 25
RfactorNum. reflection% reflection
Rfree0.443 24 -
Rwork0.344 875 -
obs--100 %
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)
15.7431.66782.71123.01822.63495.63770.0434-0.5259-0.3832-0.0447-0.3120.07330.0753-0.59760.2686-0.19120.07260.0370.03080.049-0.1149-15.9579-0.651527.9524
20.442-1.9518-0.219410.0795-0.60931.8136-0.1128-0.0999-0.26030.30230.04960.19240.54890.26660.0632-0.06550.13560.1176-0.2973-0.0097-0.0777-10.1881-28.025319.8428
36.5801-2.26892.36413.6706-0.66417.09920.04910.53010.3017-0.2892-0.3873-0.2966-0.84980.35860.33820.10460.0218-0.0158-0.11760.0529-0.1265-8.099313.585511.5595
41.8044-2.80410.22810.8031-1.25570.15490.2954-0.03460.4172-0.31320.0441-0.2536-0.13710.0653-0.33950.09340.28840.0575-0.2094-0.0466-0.1616-23.46737.903212.1993
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A34 - 143
2X-RAY DIFFRACTION2B2 - 103
3X-RAY DIFFRACTION3X34 - 140
4X-RAY DIFFRACTION4Y2 - 103

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