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- PDB-6gza: Structure of murine leukemia virus capsid C-terminal domain -

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Basic information

Entry
Database: PDB / ID: 6gza
TitleStructure of murine leukemia virus capsid C-terminal domain
ComponentsCapsid proteinCapsid
KeywordsVIRAL PROTEIN / capsid / dimer / cobalt
Function / homology
Function and homology information


retroviral 3' processing activity / host cell late endosome membrane / DNA catabolic process / virion assembly / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / ribonuclease H / protein-DNA complex / host multivesicular body / viral genome integration into host DNA / RNA-directed DNA polymerase ...retroviral 3' processing activity / host cell late endosome membrane / DNA catabolic process / virion assembly / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / ribonuclease H / protein-DNA complex / host multivesicular body / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / RNA-DNA hybrid ribonuclease activity / viral nucleocapsid / DNA recombination / structural constituent of virion / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase / nucleic acid binding / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / symbiont-mediated suppression of host gene expression / host cell plasma membrane / proteolysis / DNA binding / RNA binding / zinc ion binding / membrane
Similarity search - Function
Gag-Pol polyprotein, Zinc-finger like domain / Murine leukemia virus integrase, C-terminal / Zinc-finger like, probable DNA-binding / Murine leukemia virus (MLV) integrase (IN) C-terminal domain / Gamma-retroviral matrix protein / Gag polyprotein, inner coat protein p12 / Core shell protein Gag P30 / Matrix protein (MA), p15 / Gag polyprotein, inner coat protein p12 / Gag P30 core shell protein ...Gag-Pol polyprotein, Zinc-finger like domain / Murine leukemia virus integrase, C-terminal / Zinc-finger like, probable DNA-binding / Murine leukemia virus (MLV) integrase (IN) C-terminal domain / Gamma-retroviral matrix protein / Gag polyprotein, inner coat protein p12 / Core shell protein Gag P30 / Matrix protein (MA), p15 / Gag polyprotein, inner coat protein p12 / Gag P30 core shell protein / Gamma-retroviral matrix domain superfamily / Reverse transcriptase/retrotransposon-derived protein, RNase H-like domain / RNase H-like domain found in reverse transcriptase / RNase H / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / Ribonuclease H domain / RNase H type-1 domain profile. / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Retroviral matrix protein / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / Ribonuclease H superfamily / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
: / Putative gag polyprotein / Gag-Pol polyprotein
Similarity search - Component
Biological speciesMurine leukemia virus
MethodX-RAY DIFFRACTION / SAD / Resolution: 1.89 Å
AuthorsQu, K. / Dolezal, M. / Schur, F.K.M. / Murciano, B. / Rumlova, M. / Ruml, T. / Briggs, J.A.G.
Funding support Germany, Czech Republic, United Kingdom, 7items
OrganizationGrant numberCountry
German Research FoundationBR 3635/2-1 Germany
European Research CouncilERC-CoG-648432 Germany
Czech Science Foundation17-25602S Czech Republic
Ministry of Education (Czech Republic)LO1302 Czech Republic
Ministry of Education (Czech Republic)LO1304 Czech Republic
Ministry of Education (Czech Republic)LO1601 Czech Republic
Medical Research Council (United Kingdom)MC_UP_1201/16 United Kingdom
CitationJournal: Proc Natl Acad Sci U S A / Year: 2018
Title: Structure and architecture of immature and mature murine leukemia virus capsids.
Authors: Kun Qu / Bärbel Glass / Michal Doležal / Florian K M Schur / Brice Murciano / Alan Rein / Michaela Rumlová / Tomáš Ruml / Hans-Georg Kräusslich / John A G Briggs /
Abstract: Retroviruses assemble and bud from infected cells in an immature form and require proteolytic maturation for infectivity. The CA (capsid) domains of the Gag polyproteins assemble a protein lattice as ...Retroviruses assemble and bud from infected cells in an immature form and require proteolytic maturation for infectivity. The CA (capsid) domains of the Gag polyproteins assemble a protein lattice as a truncated sphere in the immature virion. Proteolytic cleavage of Gag induces dramatic structural rearrangements; a subset of cleaved CA subsequently assembles into the mature core, whose architecture varies among retroviruses. Murine leukemia virus (MLV) is the prototypical γ-retrovirus and serves as the basis of retroviral vectors, but the structure of the MLV CA layer is unknown. Here we have combined X-ray crystallography with cryoelectron tomography to determine the structures of immature and mature MLV CA layers within authentic viral particles. This reveals the structural changes associated with maturation, and, by comparison with HIV-1, uncovers conserved and variable features. In contrast to HIV-1, most MLV CA is used for assembly of the mature core, which adopts variable, multilayered morphologies and does not form a closed structure. Unlike in HIV-1, there is similarity between protein-protein interfaces in the immature MLV CA layer and those in the mature CA layer, and structural maturation of MLV could be achieved through domain rotations that largely maintain hexameric interactions. Nevertheless, the dramatic architectural change on maturation indicates that extensive disassembly and reassembly are required for mature core growth. The core morphology suggests that wrapping of the genome in CA sheets may be sufficient to protect the MLV ribonucleoprotein during cell entry.
History
DepositionJul 3, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 5, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 19, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Capsid protein
B: Capsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,8833
Polymers19,8242
Non-polymers591
Water3,081171
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2210 Å2
ΔGint-22 kcal/mol
Surface area9370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.198, 71.198, 77.068
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Capsid protein / Capsid


Mass: 9912.125 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Murine leukemia virus / Gene: gag
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A220A2R8, UniProt: P03355*PLUS
#2: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 171 / 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: 2.84 Å3/Da / Density % sol: 56.76 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 37 mg/ml protein, 4% PEG 3350, 0.1 M HEPES pH 8.2, 5 mM CoCl2, 5 mM CdCl2, 5 mM MgCl2 and 5 mM NiCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.89→35.6 Å / Num. obs: 39681 / % possible obs: 100 % / Redundancy: 10.2 % / Net I/σ(I): 18.9
Reflection shellResolution: 1.89→1.99 Å

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
pointlessdata scaling
SHELXDEphasing
ARP/wARPmodel building
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.89→35.599 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.18 / Phase error: 20.9
RfactorNum. reflection% reflection
Rfree0.2182 1787 5.11 %
Rwork0.1762 --
obs0.1783 34992 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.89→35.599 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1394 0 1 171 1566
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061422
X-RAY DIFFRACTIONf_angle_d0.7241918
X-RAY DIFFRACTIONf_dihedral_angle_d10.599892
X-RAY DIFFRACTIONf_chiral_restr0.046204
X-RAY DIFFRACTIONf_plane_restr0.006254
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8901-1.94120.33071700.31792533X-RAY DIFFRACTION99
1.9412-1.99830.30011480.26942541X-RAY DIFFRACTION100
1.9983-2.06280.28491380.23812533X-RAY DIFFRACTION100
2.0628-2.13660.25241440.2112577X-RAY DIFFRACTION100
2.1366-2.22210.24931600.20522511X-RAY DIFFRACTION100
2.2221-2.32320.26471230.18932558X-RAY DIFFRACTION100
2.3232-2.44570.2731090.17972589X-RAY DIFFRACTION100
2.4457-2.59890.21921500.17332539X-RAY DIFFRACTION100
2.5989-2.79940.20691260.15782557X-RAY DIFFRACTION100
2.7994-3.0810.21081430.16992587X-RAY DIFFRACTION100
3.081-3.52650.15331270.15972546X-RAY DIFFRACTION100
3.5265-4.44170.19821390.14612541X-RAY DIFFRACTION100
4.4417-35.60530.19061100.15922593X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.17560.16040.03160.1533-0.02140.05620.1203-0.12030.3134-0.3967-0.0368-0.28810.06730.1970.00070.24840.00750.0350.2509-0.020.2427-4.323338.521-6.5036
20.30620.003-0.11240.3425-0.06590.06350.0488-0.35890.08110.0825-0.0082-0.1472-0.08820.1438-0.01160.1698-0.06570.01430.2684-0.04150.1561-4.295940.25891.8068
30.6193-0.48750.76130.6425-0.45411.05410.3738-0.2295-0.1020.10670.03540.12310.0973-0.20420.41590.2171-0.0590.05390.25010.03960.1838-10.598332.64351.8356
40.0050.00650.0010.0070.0009-0.00440.14290.2256-0.6054-0.3287-0.08780.2109-0.12450.03870.00030.30990.0098-0.07440.1815-0.04640.3599-6.235422.2283-5.5967
51.01210.7838-0.08180.99280.07760.41870.1642-0.7581-0.58790.194-0.1849-0.36390.24660.09540.12880.2837-0.0173-0.03280.31510.11650.2315-4.492921.80583.8919
60.24740.1557-0.00370.17480.13250.1495-0.2075-0.0255-0.1464-0.18160.11380.02430.108-0.091-0.00620.1755-0.0380.0130.19120.03020.2138-23.623131.0068-8.748
70.3180.11430.03660.2167-0.08830.0432-0.0825-0.07720.00360.0790.03110.14660.1396-0.15470.00020.1953-0.04860.03030.221-0.00680.1874-26.102330.4303-0.5921
80.0531-0.0496-0.00180.0771-0.00940.02230.1662-0.23350.28980.0303-0.06960.0661-0.08980.29210.00120.1904-0.055-0.00440.2173-0.01530.1683-19.970237.95820.302
90.00530.0047-0.0034-0.0005-0.00530.17620.0260.23330.4634-0.238-0.0422-0.18130.13680.24540.01220.2338-0.0280.01440.21060.09950.3477-21.081848.2135-8.8795
101.71820.21020.11770.3323-0.34520.50710.282-0.60410.91550.1512-0.12840.5174-0.1216-0.26530.15510.22970.00240.04470.2422-0.08080.4841-26.625248.6031-0.4788
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 18 )
2X-RAY DIFFRACTION2chain 'A' and (resid 19 through 40 )
3X-RAY DIFFRACTION3chain 'A' and (resid 41 through 54 )
4X-RAY DIFFRACTION4chain 'A' and (resid 55 through 64 )
5X-RAY DIFFRACTION5chain 'A' and (resid 65 through 87 )
6X-RAY DIFFRACTION6chain 'B' and (resid 1 through 18 )
7X-RAY DIFFRACTION7chain 'B' and (resid 19 through 40 )
8X-RAY DIFFRACTION8chain 'B' and (resid 41 through 54 )
9X-RAY DIFFRACTION9chain 'B' and (resid 55 through 65 )
10X-RAY DIFFRACTION10chain 'B' and (resid 66 through 87 )

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