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- PDB-2xg7: Crystal Structure of BST2-Tetherin Ectodomain expressed in HEK293... -

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Basic information

Entry
Database: PDB / ID: 2xg7
TitleCrystal Structure of BST2-Tetherin Ectodomain expressed in HEK293T cells
ComponentsBONE MARROW STROMAL ANTIGEN 2
KeywordsANTIVIRAL PROTEIN / INNATE IMMUNE FACTOR
Function / homology
Function and homology information


negative regulation of plasmacytoid dendritic cell cytokine production / negative regulation of intracellular transport of viral material / response to interferon-beta / response to interferon-alpha / metalloendopeptidase inhibitor activity / positive regulation of leukocyte proliferation / azurophil granule membrane / negative regulation of viral genome replication / B cell activation / response to type II interferon ...negative regulation of plasmacytoid dendritic cell cytokine production / negative regulation of intracellular transport of viral material / response to interferon-beta / response to interferon-alpha / metalloendopeptidase inhibitor activity / positive regulation of leukocyte proliferation / azurophil granule membrane / negative regulation of viral genome replication / B cell activation / response to type II interferon / side of membrane / multivesicular body / negative regulation of cell migration / regulation of actin cytoskeleton organization / negative regulation of cell growth / response to virus / SARS-CoV-1 activates/modulates innate immune responses / Interferon alpha/beta signaling / defense response to virus / positive regulation of canonical NF-kappaB signal transduction / apical plasma membrane / membrane raft / innate immune response / intracellular membrane-bounded organelle / Neutrophil degranulation / cell surface / Golgi apparatus / protein homodimerization activity / RNA binding / extracellular exosome / identical protein binding / membrane / plasma membrane
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1700 / Bone marrow stromal antigen 2 / Bone marrow stromal antigen 2 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Bone marrow stromal antigen 2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.45 Å
AuthorsSteiner, R.A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Structural and Functional Studies on the Extracellular Domain of Bst2/Tetherin in Reduced and Oxidized Conformations.
Authors: Schubert, H.L. / Zhai, Q. / Sandrin, V. / Eckert, D.M. / Garcia-Maya, M. / Saul, L. / Sundquist, W.I. / Steiner, R.A. / Hill, C.P.
History
DepositionMay 31, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 13, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Dec 20, 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
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Oct 9, 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: BONE MARROW STROMAL ANTIGEN 2
C: BONE MARROW STROMAL ANTIGEN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3704
Polymers22,9282
Non-polymers4422
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3930 Å2
ΔGint-34.1 kcal/mol
Surface area11320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)28.860, 91.860, 146.960
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 BONE MARROW STROMAL ANTIGEN 2 / BST2 / TETHERIN / HM1.24 ANTIGEN / CD317


Mass: 11463.895 Da / Num. of mol.: 2 / Fragment: ECTODOMAIN, RESIDUES 51-151
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PHLSEC / Cell (production host): HUMAN EMBRYONIC KIDNEY CELLS / Cell line (production host): HEK293T / Production host: HOMO SAPIENS (human) / References: UniProt: Q10589
#2: 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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
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
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: 4.2 Å3/Da / Density % sol: 70 % / Description: NONE
Crystal growpH: 8.5 / Details: 8% PEG8000, 0.1M TRIS-HCL PH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9763
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 30, 2010 / Details: MIRRORS
RadiationMonochromator: SI (111) DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 3.45→38.95 Å / Num. obs: 5576 / % possible obs: 99.2 % / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 8.9
Reflection shellResolution: 3.45→3.64 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.71 / Mean I/σ(I) obs: 2.5 / % possible all: 99.4

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Processing

Software
NameVersionClassification
REFMAC5.6.0074refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3MKX

3mkx
PDB Unreleased entry


Resolution: 3.45→77.89 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.929 / SU B: 62.942 / SU ML: 0.417 / Cross valid method: THROUGHOUT / ESU R: 1.768 / ESU R Free: 0.507 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DISORDERED SIDE-CHAINS WERE MODELED STEREOCHEMICALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.29795 250 4.5 %RANDOM
Rwork0.26912 ---
obs0.27038 5303 98.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 71.784 Å2
Baniso -1Baniso -2Baniso -3
1--8.69 Å20 Å20 Å2
2--4.06 Å2-0 Å2
3---4.63 Å2
Refinement stepCycle: LAST / Resolution: 3.45→77.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1209 0 28 0 1237
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0211244
X-RAY DIFFRACTIONr_bond_other_d0.0040.02828
X-RAY DIFFRACTIONr_angle_refined_deg1.3791.9821670
X-RAY DIFFRACTIONr_angle_other_deg2.04932035
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.1945155
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.17726.50863
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.52315242
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.057158
X-RAY DIFFRACTIONr_chiral_restr0.060.2199
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021379
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02207
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
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: 3.45→3.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.528 18 -
Rwork0.348 391 -
obs--98.55 %
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)
12.0784-5.01745.93519.2423-22.337626.9451-0.1841-0.25540.05010.47040.1969-0.2837-0.4367-0.5101-0.01280.1359-0.10790.08750.2967-0.11680.3615-6.9196-21.539646.2363
20.82410.4326-0.471830.9815-32.428734.9377-0.2879-0.0885-0.094-0.367-0.388-1.02020.51080.05980.67590.1101-0.0038-0.01250.3131-0.02840.3638-5.3133-23.437940.9578
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A72 - 153
2X-RAY DIFFRACTION2C77 - 151

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