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- PDB-6br9: Structure of A6 reveals a novel lipid transporter -

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Basic information

Entry
Database: PDB / ID: 6br9
TitleStructure of A6 reveals a novel lipid transporter
ComponentsProtein A6 homolog
KeywordsLIPID BINDING 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: 2.2 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 / Source and taxonomy
Category: citation / citation_author ...citation / citation_author / entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _entity_src_gen.pdbx_gene_src_scientific_name / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.seq_align_beg
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
Revision 1.5Mar 13, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein A6 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3536
Polymers41,7321
Non-polymers3,6215
Water91951
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.699, 74.151, 143.571
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-547-

HOH

21A-549-

HOH

31A-551-

HOH

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Components

#1: Protein Protein A6 homolog


Mass: 41731.785 Da / Num. of mol.: 1
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.: 4 / 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.: 1 / Source method: obtained synthetically / Formula: C40H77O10P / Comment: phospholipid*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 51 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsSome of the atoms in 6OU and PGV are disordered. Hence they have been modeled with zero occupancy

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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: 2.48 Å3/Da / Density % sol: 50.34 %
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: 0.97921 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: 0.97921 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 89447 / % possible obs: 99.3 % / Redundancy: 5.9 % / Rsym value: 0.085 / Net I/σ(I): 18.5
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 2.6 / Rsym value: 0.759 / % possible all: 95.5

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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: 2.2→37.53 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.36
RfactorNum. reflection% reflection
Rfree0.27 1517 10 %
Rwork0.216 --
obs0.221 15169 98.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.2→37.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1917 0 247 51 2215
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092187
X-RAY DIFFRACTIONf_angle_d0.92882
X-RAY DIFFRACTIONf_dihedral_angle_d24.0661368
X-RAY DIFFRACTIONf_chiral_restr0.052318
X-RAY DIFFRACTIONf_plane_restr0.005334
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1931-2.26390.31991200.28451084X-RAY DIFFRACTION91
2.2639-2.34480.31921350.25021214X-RAY DIFFRACTION98
2.3448-2.43870.29631390.2411252X-RAY DIFFRACTION100
2.4387-2.54960.2911380.22121234X-RAY DIFFRACTION100
2.5496-2.6840.28981370.23021234X-RAY DIFFRACTION100
2.684-2.85210.26641390.2141253X-RAY DIFFRACTION100
2.8521-3.07230.25921400.21951260X-RAY DIFFRACTION100
3.0723-3.38120.30331380.22561234X-RAY DIFFRACTION100
3.3812-3.87010.26561400.20771267X-RAY DIFFRACTION100
3.8701-4.87420.27531420.18991272X-RAY DIFFRACTION100
4.8742-37.53070.24311490.22031348X-RAY DIFFRACTION100
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)
16.7011-1.7794-0.38431.63462.92676.94590.95790.05970.3995-0.25630.01830.3754-0.6825-0.4081-1.03441.1628-0.04790.15050.5260.13990.708124.645914.73922.2488
25.518-0.48761.05564.3025-1.42373.20990.022-2.3118-0.07110.60380.8457-0.776-0.4177-0.0823-0.37430.7452-0.11050.2230.8007-0.22960.424232.458413.915632.6692
34.2018-1.3166-3.38228.2838-0.5388.5767-0.25260.0544-0.874-0.0083-0.12241.36830.4933-1.33480.4820.5896-0.15960.00440.37410.03670.594624.64864.803412.4155
45.72980.99520.08423.2714-0.21471.22430.26290.2746-1.4350.0383-0.1634-0.51160.40750.6394-0.04160.6012-0.0170.04770.43470.2330.513636.9473-2.140918.1136
57.78583.8679-0.34357.4480.58083.1188-0.159-1.8784-0.55180.58350.0109-1.46690.67590.1031-0.04850.9271-0.1259-0.07191.0048-0.03840.471943.88937.647434.1953
65.4926-0.3153-0.04789.4864-7.86219.3998-0.0793-1.4263-0.27042.4387-0.1742-0.8808-1.8427-0.10330.45090.6887-0.153-0.11650.63220.10540.537749.232914.307525.9863
75.08090.33196.83473.6445-0.80929.3725-0.5420.28951.3531-0.2276-0.00550.2128-0.59570.27740.65530.3247-0.06110.04820.26510.00180.596143.68625.10885.133
85.3607-1.058-2.10843.4871-0.62423.52140.56650.5234-0.78220.84380.0951-1.36160.5312-0.249-0.1240.9161-0.0435-0.31010.254-0.08250.881124.64529.21066.3399
99.1925-2.4961-0.57422.5267-1.41671.426-0.03990.25890.06160.26890.0615-0.0225-0.1822-0.0254-0.02740.3953-0.0125-0.00180.12780.00640.396838.85515.45895.1957
101.30180.145-1.23964.5848-1.55325.33590.0938-0.1936-0.46640.1506-0.0704-0.66370.36970.4135-0.1760.39760.0552-0.03340.32670.12790.531948.86753.445911.441
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 127 THROUGH 145 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 146 THROUGH 176 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 177 THROUGH 195 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 196 THROUGH 225 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 226 THROUGH 255 )
6X-RAY DIFFRACTION6CHAIN 'A' AND (RESID 256 THROUGH 276 )
7X-RAY DIFFRACTION7CHAIN 'A' AND (RESID 277 THROUGH 294 )
8X-RAY DIFFRACTION8CHAIN 'A' AND (RESID 295 THROUGH 307 )
9X-RAY DIFFRACTION9CHAIN 'A' AND (RESID 308 THROUGH 347 )
10X-RAY DIFFRACTION10CHAIN 'A' AND (RESID 348 THROUGH 374 )

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