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- PDB-6br8: Structure of A6 reveals a novel lipid transporter -

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Basic information

Entry
Database: PDB / ID: 6br8
TitleStructure of A6 reveals a novel lipid transporter
ComponentsProtein A6 homolog
KeywordsVIRAL PROTEIN / poxvirus / A6 / lipid binding / membrane biogenesis
Function / homologyPoxvirus A6 / Poxvirus A6 protein / virion component / Chem-6OU / Chem-PGV / Protein A6 homolog
Function and homology information
Biological speciesFowlpox virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsDeng, J. / Peng, S. / Pathak, P.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI 133589 United States
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Structure of a lipid-bound viral membrane assembly protein reveals a modality for enclosing the lipid bilayer.
Authors: Pathak, P.K. / Peng, S. / Meng, X. / Han, Y. / Zhang, B. / Zhang, F. / Xiang, Y. / Deng, J.
History
DepositionNov 30, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 20, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 4, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jul 18, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein A6 homolog
B: Protein A6 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,49112
Polymers59,2492
Non-polymers7,24210
Water68538
1
A: Protein A6 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2466
Polymers29,6251
Non-polymers3,6215
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Protein A6 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2466
Polymers29,6251
Non-polymers3,6215
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.909, 75.163, 148.380
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 Protein A6 homolog


Mass: 29624.529 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fowlpox virus (strain NVSL) / Strain: NVSL / Gene: FPV170 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9J563
#2: Chemical
ChemComp-6OU / [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate


Mass: 717.996 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C39H76NO8P / Comment: phospholipid*YM
#3: Chemical ChemComp-PGV / (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE / PHOSPHATIDYLGLYCEROL, 2-VACCENOYL-1-PALMITOYL-SN-GLYCEROL-3-PHOSPHOGLYCEROL / Phosphatidylglycerol


Mass: 749.007 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C40H77O10P / Comment: phospholipid*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 2.6 Å3/Da / Density % sol: 52.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2M sodium thiocyanate, 25% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97935 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Mar 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97935 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 50967 / % possible obs: 98.6 % / Redundancy: 5.8 % / Rsym value: 0.056 / Net I/σ(I): 21.6
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 5.7 % / Mean I/σ(I) obs: 1.2 / Num. unique obs: 2648 / Rsym value: 0.985 / % possible all: 96.2

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.3→44.338 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 33.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2891 3721 7.32 %
Rwork0.2282 --
obs0.2326 50849 96.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→44.338 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4086 0 494 38 4618
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114633
X-RAY DIFFRACTIONf_angle_d1.2236118
X-RAY DIFFRACTIONf_dihedral_angle_d20.6132890
X-RAY DIFFRACTIONf_chiral_restr0.064672
X-RAY DIFFRACTIONf_plane_restr0.006714
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3001-2.32920.35111230.33741514X-RAY DIFFRACTION83
2.3292-2.35980.37381320.32121703X-RAY DIFFRACTION95
2.3598-2.39220.31341390.31651749X-RAY DIFFRACTION95
2.3922-2.42630.34761370.3021703X-RAY DIFFRACTION95
2.4263-2.46260.31091430.30141766X-RAY DIFFRACTION96
2.4626-2.5010.32051370.29411710X-RAY DIFFRACTION96
2.501-2.5420.32941340.2841697X-RAY DIFFRACTION96
2.542-2.58590.30931390.28221754X-RAY DIFFRACTION96
2.5859-2.63290.31081370.27561757X-RAY DIFFRACTION97
2.6329-2.68350.32211300.29161703X-RAY DIFFRACTION95
2.6835-2.73830.33611310.26011610X-RAY DIFFRACTION88
2.7383-2.79780.31231350.27311720X-RAY DIFFRACTION96
2.7978-2.86290.29471400.26961751X-RAY DIFFRACTION98
2.8629-2.93450.35161390.26971766X-RAY DIFFRACTION97
2.9345-3.01380.33891420.25741819X-RAY DIFFRACTION98
3.0138-3.10250.31921400.27681739X-RAY DIFFRACTION98
3.1025-3.20260.37541390.25871783X-RAY DIFFRACTION98
3.2026-3.3170.34461380.24821781X-RAY DIFFRACTION99
3.317-3.44980.29181400.23521786X-RAY DIFFRACTION99
3.4498-3.60670.32541380.23421805X-RAY DIFFRACTION99
3.6067-3.79670.29721450.21541783X-RAY DIFFRACTION100
3.7967-4.03450.28181370.21141750X-RAY DIFFRACTION96
4.0345-4.34570.2251420.18711785X-RAY DIFFRACTION100
4.3457-4.78260.24461440.18321809X-RAY DIFFRACTION100
4.7826-5.47360.28241410.19821833X-RAY DIFFRACTION100
5.4736-6.89190.27831410.24021799X-RAY DIFFRACTION100
6.8919-44.34630.24751380.18641753X-RAY DIFFRACTION97
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)
12.7346-2.4307-0.23336.19541.60872.82360.2764-0.5099-0.2640.6003-0.56280.6354-0.3762-0.82380.1820.6050.09740.05710.73340.05240.5098-41.3225.5604-50.557
24.22970.47752.18158.98391.94778.60070.324-0.8308-0.0973-0.23050.0517-0.0432-0.2655-1.217-0.06740.4695-0.03860.14620.73960.15930.4394-39.316418.9046-47.78
33.70581.15650.33624.86020.30463.81660.3286-0.6772-0.17530.4481-0.2288-0.20120.46080.2143-0.10810.52050.0080.01250.67450.17560.5383-28.043312.0966-44.7961
43.06280.87682.10862.8663-2.81245.9831-0.2984-0.49130.25410.29430.0208-0.5703-0.7988-0.19560.53650.48550.07550.06010.5192-0.04560.6219-22.424624.5536-59.0617
52.3051-3.24491.11998.99470.85151.60830.1968-0.24681.22610.46960.04140.5623-0.0129-0.33770.25280.5413-0.10150.03350.71360.08970.8818-43.775530.2462-71.7304
66.4155-5.55491.23994.8018-0.07483.8390.06580.6083-0.9952-0.247-0.05780.56340.3903-0.5173-0.14990.4505-0.0192-0.02760.33210.10740.6569-38.537117.5094-70.3024
76.6688-0.3329-0.3533.9929-1.03337.6457-0.0602-0.6262-0.35830.1635-0.0856-0.72070.59120.54620.08910.36520.1056-0.04050.3760.05780.4819-19.083811.137-61.0693
83.9469-0.37353.35745.3765-5.16427.87430.2752-0.23230.0549-0.782-0.1129-0.8883-0.37411.0617-0.0890.9599-0.16320.1670.8398-0.02480.574612.457425.4553-23.5607
93.0952-0.2680.3554.599-1.48233.76210.0330.4167-0.0359-0.7053-0.0037-0.04820.29070.31240.01340.5954-0.02430.10740.4878-0.10420.34183.74415.0043-28.0827
103.56030.22951.46492.40220.38463.3264-0.1173-0.07510.286-0.0166-0.0954-0.1013-0.0055-0.04360.13150.33270.03860.0610.3670.01330.4826-2.30518.9977-10.5825
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 126 through 152 )
2X-RAY DIFFRACTION2chain 'A' and (resid 153 through 195 )
3X-RAY DIFFRACTION3chain 'A' and (resid 196 through 255 )
4X-RAY DIFFRACTION4chain 'A' and (resid 256 through 293 )
5X-RAY DIFFRACTION5chain 'A' and (resid 294 through 307 )
6X-RAY DIFFRACTION6chain 'A' and (resid 308 through 332 )
7X-RAY DIFFRACTION7chain 'A' and (resid 333 through 374 )
8X-RAY DIFFRACTION8chain 'B' and (resid 126 through 152 )
9X-RAY DIFFRACTION9chain 'B' and (resid 153 through 255 )
10X-RAY DIFFRACTION10chain 'B' and (resid 256 through 374 )

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