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- PDB-4arg: Structure of the immature retroviral capsid at 8A resolution by c... -

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Basic information

Entry
Database: PDB / ID: 4arg
TitleStructure of the immature retroviral capsid at 8A resolution by cryo- electron microscopy
DescriptorM-PMV DPRO CANC PROTEIN
KeywordsVIRAL PROTEIN / RETROVIRUS
Specimen sourceMASON-PFIZER MONKEY VIRUS / virus
MethodElectron microscopy (7 Å resolution / Helical array / Helical)
AuthorsBharat, T.A.M. / Davey, N.E. / Ulbrich, P. / Riches, J.D. / Marco, A.D. / Rumlova, M. / Sachse, C. / Ruml, T. / Briggs, J.A.G.
CitationNature, 2012, 487, 385-389

Nature, 2012, 487, 385-389 StrPapers
Structure of the immature retroviral capsid at 8 Å resolution by cryo-electron microscopy.
Tanmay A M Bharat / Norman E Davey / Pavel Ulbrich / James D Riches / Alex de Marco / Michaela Rumlova / Carsten Sachse / Tomas Ruml / John A G Briggs

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Apr 23, 2012 / Release: May 30, 2012
RevisionDateData content typeGroupProviderType
1.0May 30, 2012Structure modelrepositoryInitial release
1.1Aug 1, 2012Structure modelDatabase references

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Assembly

Deposited unit
A: M-PMV DPRO CANC PROTEIN
B: M-PMV DPRO CANC PROTEIN
C: M-PMV DPRO CANC PROTEIN
D: M-PMV DPRO CANC PROTEIN


Theoretical massNumber of molelcules
Total (without water)44,2194
Polyers44,2194
Non-polymers00
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Polypeptide(L)M-PMV DPRO CANC PROTEIN / Coordinate model: Cα atoms only


Mass: 14371.477 Da / Num. of mol.: 2 / Fragment: M-PMV CA-NTD DIMER, RESIDUES 149-277 / Source: (gene. exp.) MASON-PFIZER MONKEY VIRUS / virus

Biological process

#2: Polypeptide(L)M-PMV DPRO CANC PROTEIN / Coordinate model: Cα atoms only


Mass: 7737.796 Da / Num. of mol.: 2 / Fragment: M-PMV CA-NTD DIMER, RESIDUES 283-351 / Source: (gene. exp.) MASON-PFIZER MONKEY VIRUS / virus

Biological process

Sequence detailsTHIS ENTRY FITS THE STRUCTURE OF HIV (UNP Q72497) INTO THE ELCTRON DENSITY MAP OF MPMV (EM 2089). THE CYCLOPHILIN BINDING LOOP OF HIV-1 (PVHAGPIAPGQMREP) AND THE SEQUENCE OF RESIDUES (SPTSI) IN THE INTER-DOMAIN LINKER WERE NOT INCLUDED FOR THE FITTING.

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: HELICAL ARRAY / Reconstruction method: HELICAL

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Sample preparation

ComponentName: M-PMV CANC GAG TUBES / Type: COMPLEX
Buffer solutionName: 100MM NACL, 50MM TRIS-HCL, 1UM ZN / Details: 100MM NACL, 50MM TRIS-HCL, 1UM ZN / pH: 7.7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: HOLEY CARBON
VitrificationCryogen name: ETHANE / Details: LIQUID ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS / Date: Jul 5, 2011
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 47000 / Nominal defocus max: 4000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm
Image recordingElectron dose: 0.2 e/Å2 / Film or detector model: KODAK SO-163 FILM
Image scansNumber digital images: 46
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameCategory
1UCSF ChimeraMODEL FITTING
2AV3RECONSTRUCTION
3SPIDERRECONSTRUCTION
CTF correctionDetails: DIVISION BY 3D CTF SQ
3D reconstructionMethod: REAL SPACE HELICAL RECONSTRUCTION WITH 3D ASYMMETRIC UNIT AVERAGING.
Resolution: 7 Å / Nominal pixel size: 1.53 / Actual pixel size: 1.53
Details: REAL SPACE HELICAL RECONSTRUCTION WITH 3D ASYMMETRIC UNIT AVERAGING. SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2089. (DEPOSITION ID: 10767).
Symmetry type: HELICAL
Atomic model buildingDetails: METHOD--RIGID BODY REFINEMENT PROTOCOL--NMR,XRAY / Ref protocol: RIGID BODY FIT / Ref space: REAL
Atomic model building
IDPDB-ID 3D fitting ID
11L6N1
22KGF1
Least-squares processHighest resolution: 7 Å
Refine hist #LASTHighest resolution: 7 Å
Number of atoms included #LASTProtein: 366 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 366

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