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- PDB-2x7a: Structural basis of HIV-1 tethering to membranes by the Bst2-teth... -

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Basic information

Entry
Database: PDB / ID: 2x7a
TitleStructural basis of HIV-1 tethering to membranes by the Bst2-tetherin ectodomain
ComponentsBONE MARROW STROMAL ANTIGEN 2
KeywordsIMMUNE SYSTEM / TETHERIN / GPI-ANCHOR / ANTIVIRAL DEFENSE / B-CELL ACTIVATION / SIGNAL-ANCHOR
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 / response to virus / negative regulation of cell growth / SARS-CoV-1 activates/modulates innate immune responses / Interferon alpha/beta signaling / positive regulation of canonical NF-kappaB signal transduction / defense response to virus / membrane raft / apical plasma membrane / intracellular membrane-bounded organelle / innate immune response / Neutrophil degranulation / Golgi apparatus / cell surface / protein homodimerization activity / RNA binding / extracellular exosome / membrane / identical protein binding / 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 / SAD / Resolution: 2.77 Å
AuthorsNatrajan, G. / McCarthy, A.A. / Weissenhorn, W.
CitationJournal: Cell Host Microbe / Year: 2010
Title: Structural Basis of HIV-1 Tethering to Membranes by the Bst-2/Tetherin Ectodomain.
Authors: Hinz, A. / Miguet, N. / Natrajan, G. / Usami, Y. / Yamanaka, H. / Renesto, P. / Hartlieb, B. / Mccarthy, A.A. / Simorre, J.P. / Gottlinger, H. / Weissenhorn, W.
History
DepositionFeb 25, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 28, 2010Provider: repository / Type: Initial release
Revision 1.1Jun 2, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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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
B: BONE MARROW STROMAL ANTIGEN 2
C: BONE MARROW STROMAL ANTIGEN 2
D: BONE MARROW STROMAL ANTIGEN 2
E: BONE MARROW STROMAL ANTIGEN 2
F: BONE MARROW STROMAL ANTIGEN 2
G: BONE MARROW STROMAL ANTIGEN 2
H: BONE MARROW STROMAL ANTIGEN 2
I: BONE MARROW STROMAL ANTIGEN 2
J: BONE MARROW STROMAL ANTIGEN 2
K: BONE MARROW STROMAL ANTIGEN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,36527
Polymers75,83911
Non-polymers52516
Water1,08160
1
A: BONE MARROW STROMAL ANTIGEN 2
B: BONE MARROW STROMAL ANTIGEN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8474
Polymers13,7892
Non-polymers582
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2820 Å2
ΔGint-39.5 kcal/mol
Surface area8750 Å2
MethodPISA
2
C: BONE MARROW STROMAL ANTIGEN 2
D: BONE MARROW STROMAL ANTIGEN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8123
Polymers13,7892
Non-polymers231
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1980 Å2
ΔGint-34.8 kcal/mol
Surface area8000 Å2
MethodPISA
3
E: BONE MARROW STROMAL ANTIGEN 2
F: BONE MARROW STROMAL ANTIGEN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8835
Polymers13,7892
Non-polymers943
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3000 Å2
ΔGint-55.8 kcal/mol
Surface area8380 Å2
MethodPISA
4
G: BONE MARROW STROMAL ANTIGEN 2
H: BONE MARROW STROMAL ANTIGEN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0338
Polymers13,7892
Non-polymers2446
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3010 Å2
ΔGint-78.9 kcal/mol
Surface area7960 Å2
MethodPISA
5
I: BONE MARROW STROMAL ANTIGEN 2
J: BONE MARROW STROMAL ANTIGEN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8956
Polymers13,7892
Non-polymers1064
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2800 Å2
ΔGint-38.8 kcal/mol
Surface area8640 Å2
MethodPISA
6
K: BONE MARROW STROMAL ANTIGEN 2

K: BONE MARROW STROMAL ANTIGEN 2


Theoretical massNumber of molelcules
Total (without water)13,7892
Polymers13,7892
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_657-x+1,y,-z+21
Buried area1000 Å2
ΔGint-10.1 kcal/mol
Surface area6290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)169.890, 85.930, 123.310
Angle α, β, γ (deg.)90.00, 126.94, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 11 molecules ABCDEFGHIJK

#1: Protein
BONE MARROW STROMAL ANTIGEN 2 / HM1.24 ANTIGEN / BST-2 / CD317 / TETHERIN


Mass: 6894.455 Da / Num. of mol.: 11 / Fragment: RESIDUES 87-147
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ROSETTA2 / References: UniProt: Q10589

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Non-polymers , 5 types, 76 molecules

#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 7 / 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.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 2.2 Å3/Da / Density % sol: 43.84 % / Description: NONE
Crystal growpH: 5
Details: 0.02M MGCL2, 0.1M BIS TRIS PH5.0, 20% POLYACRYLIC ACID

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.979
DetectorType: ADSC CCD / Detector: CCD / Date: Jun 1, 2009 / Details: MIRRORS
RadiationMonochromator: CHANNEL CUT ESRF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.77→45 Å / Num. obs: 35553 / % possible obs: 98.1 % / Observed criterion σ(I): 1.5 / Redundancy: 7.6 % / Biso Wilson estimate: 61.42 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 13.8
Reflection shellResolution: 2.77→2.92 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 3.8 / % possible all: 97.7

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
SHARPphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.77→44.88 Å / SU ML: 0.44 / σ(F): 1.35 / Phase error: 28.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2728 1775 5 %
Rwork0.2364 --
obs0.2383 35361 97.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 62.917 Å2 / ksol: 0.323 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--4.7737 Å20 Å23.9413 Å2
2--0.2451 Å20 Å2
3---4.5286 Å2
Refinement stepCycle: LAST / Resolution: 2.77→44.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4592 0 21 60 4673
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114612
X-RAY DIFFRACTIONf_angle_d1.2416170
X-RAY DIFFRACTIONf_dihedral_angle_d21.0881755
X-RAY DIFFRACTIONf_chiral_restr0.082750
X-RAY DIFFRACTIONf_plane_restr0.003809
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.77-2.84490.35171210.29992540X-RAY DIFFRACTION96
2.8449-2.92860.35341310.30162551X-RAY DIFFRACTION97
2.9286-3.02310.34291520.28972563X-RAY DIFFRACTION98
3.0231-3.13120.27651470.26842554X-RAY DIFFRACTION98
3.1312-3.25650.31971300.25232607X-RAY DIFFRACTION98
3.2565-3.40460.27331370.25542594X-RAY DIFFRACTION98
3.4046-3.58410.27961450.23452569X-RAY DIFFRACTION98
3.5841-3.80850.2291280.19672597X-RAY DIFFRACTION98
3.8085-4.10240.22561240.1952609X-RAY DIFFRACTION98
4.1024-4.51490.24991320.19532640X-RAY DIFFRACTION98
4.5149-5.16740.25011420.20272596X-RAY DIFFRACTION98
5.1674-6.50720.35161370.27492629X-RAY DIFFRACTION98
6.5072-44.88630.22141490.20992537X-RAY DIFFRACTION93
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)
17.1925-4.48762.8392.851-2.22371.11911.36431.4859-0.1549-1.0291-1.06770.11630.90870.7661-0.33890.49260.1862-0.10440.4728-0.12830.220718.956572.479332.2571
24.329-1.20730.98340.9935-1.04661.0867-0.2639-0.25850.2630.14380.12960.1103-0.1136-0.38640.10980.35090.1325-0.03020.2914-0.08370.253916.229475.230738.2546
30.92560.2119-0.85730.5144-0.47421.14040.2287-0.31720.09670.232-0.17910.49580.0371-1.07480.16050.16590.156-0.00560.67670.00980.39470.88756.151668.1917
41.8482-0.75610.00750.17060.69880.6260.08510.8817-0.6491-0.0035-0.0898-0.01420.03760.1116-0.11770.2166-0.1382-0.00890.5808-0.12530.26364.003250.634162.6408
50.81722.29830.92597.93963.26271.47290.13220.09420.04131.45390.03920.06220.3757-0.092-0.03390.4135-0.05950.00180.1468-0.02410.061640.891889.503785.6778
61.54552.420.22444.59411.52560.4685-0.43670.14250.228-1.08120.43470.2031-0.48050.17750.03010.5397-0.05780.00490.15750.04150.229741.8992.763479.0345
71.43-1.4968-0.05492.4542-0.90522.0144-0.18230.029-0.3632-0.1576-0.0350.21410.71430.11770.14920.5504-0.05780.090.2048-0.03510.353745.28131.962468.6188
80.3097-0.3462-0.771.498-1.0691.2713-0.1625-0.03340.1543-0.1785-0.3007-0.8280.39190.18860.48030.2497-0.01760.1060.12550.12070.197252.336433.502966.1807
93.2284-4.88170.95857.5973-3.19842.2926-0.1487-0.45570.6068-0.20170.1131-1.02650.10140.18810.2230.12690.0169-0.14210.2235-0.0130.291441.946337.1231102.5858
106.9643-8.10285.94977.6311-6.42836.15770.3704-0.3026-1.0245-0.20120.30820.96560.19540.048-0.43830.0701-0.0414-0.02620.15120.2460.391136.548234.2854106.1507
113.53480.56581.22320.490.23182.4648-0.3660.21151.2655-1.41960.0101-0.54-0.5567-0.28220.31860.81950.22070.25840.26630.07620.78049.201678.279392.9157
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN C
4X-RAY DIFFRACTION4CHAIN D
5X-RAY DIFFRACTION5CHAIN E
6X-RAY DIFFRACTION6CHAIN F
7X-RAY DIFFRACTION7CHAIN G
8X-RAY DIFFRACTION8CHAIN H
9X-RAY DIFFRACTION9CHAIN I
10X-RAY DIFFRACTION10CHAIN J
11X-RAY DIFFRACTION11CHAIN K

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