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- PDB-2y4z: Structure of the amino-terminal capsid restriction escape mutatio... -

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Basic information

Entry
Database: PDB / ID: 2y4z
TitleStructure of the amino-terminal capsid restriction escape mutation N- MLV L10W
ComponentsCAPSID PROTEIN P30
KeywordsVIRAL PROTEIN / RESTRICTION
Function / homology
Function and homology information


viral budding via host ESCRT complex / host multivesicular body / viral nucleocapsid / structural constituent of virion / host cell plasma membrane / RNA binding / zinc ion binding / membrane
Similarity search - Function
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 / Human Immunodeficiency Virus Type 1 Capsid Protein / Human Immunodeficiency Virus Type 1 Capsid Protein / Retroviral matrix protein ...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 / Human Immunodeficiency Virus Type 1 Capsid Protein / Human Immunodeficiency Virus Type 1 Capsid Protein / 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. / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesMURINE LEUKEMIA VIRUS
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.001 Å
AuthorsGoldstone, D.C. / Holden-Dye, K. / Ohkura, S. / Stoye, J.P. / Taylor, I.A.
CitationJournal: Plos Pathog. / Year: 2011
Title: Novel Escape Mutants Suggest an Extensive Trim5Alpha Binding Site Spanning the Entire Outer Surface of the Murine Leukemia Virus Capsid Protein.
Authors: Ohkura, S. / Goldstone, D.C. / Yap, M.W. / Holden-Dye, K. / Taylor, I.A. / Stoye, J.P.
History
DepositionJan 11, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 23, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 650 HELIX DETERMINATION METHOD: PROVIDED BY DEPOSITOR
Remark 700 SHEET DETERMINATION METHOD: PROVIDED BY DEPOSITOR

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CAPSID PROTEIN P30
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,1982
Polymers16,1061
Non-polymers921
Water1,78399
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)71.880, 33.647, 59.320
Angle α, β, γ (deg.)90.00, 111.91, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2002-

HOH

21A-2080-

HOH

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Components

#1: Protein CAPSID PROTEIN P30 / / CA


Mass: 16105.835 Da / Num. of mol.: 1 / Fragment: N-TERMINAL DOMAIN, RESIDUES 215-346 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MURINE LEUKEMIA VIRUS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P03336
#2: 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
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 99 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, LEU 224 TO TRP
Sequence detailsTHE MUTATION MENTIONED IN REMARK 400 AND THE SEQADV RECORD CORRESPONDS TO RESIDUE 10 OF THE PROTEIN SEQUENCE.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.06 Å3/Da / Density % sol: 40 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→25 Å / Num. obs: 9015 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Biso Wilson estimate: 29.07 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 25.1
Reflection shellResolution: 2→2.07 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.18 / Mean I/σ(I) obs: 6.3 / % possible all: 97

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1U7K (CHAIN A)

1u7k


Resolution: 2.001→24.681 Å / SU ML: 0.25 / σ(F): 1.34 / Phase error: 22.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2438 428 4.8 %
Rwork0.1742 --
obs0.1774 9013 99.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.319 Å2 / ksol: 0.364 e/Å3
Displacement parametersBiso mean: 36.3 Å2
Baniso -1Baniso -2Baniso -3
1-0.1625 Å20 Å25.4381 Å2
2---4.1237 Å20 Å2
3---3.9611 Å2
Refinement stepCycle: LAST / Resolution: 2.001→24.681 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1080 0 6 99 1185
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091122
X-RAY DIFFRACTIONf_angle_d0.9771530
X-RAY DIFFRACTIONf_dihedral_angle_d17.367415
X-RAY DIFFRACTIONf_chiral_restr0.071162
X-RAY DIFFRACTIONf_plane_restr0.005203
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0008-2.29020.26631460.17972774X-RAY DIFFRACTION98
2.2902-2.88470.2621410.16692855X-RAY DIFFRACTION100
2.8847-24.68260.22641410.17282956X-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)
13.6652-0.6585-2.3099.27445.88044.92350.06330.2692-0.27831.0112-0.51960.30720.5658-0.39010.310.1907-0.0227-0.01440.17270.03480.245429.2748-10.45745.0534
21.4498-1.7811-0.53152.20470.53140.70340.0096-0.0667-0.33940.27650.05690.5445-0.0665-0.1528-0.07810.15970.0430.01790.27480.03450.301114.89673.19525.5167
32.6921.0692-1.75070.6278-0.91332.63830.4584-0.3887-0.46770.482-0.3520.4526-0.4944-0.2664-0.18140.36150.01170.10110.2770.08670.261417.02486.370616.6209
42.8547-0.84130.57291.25931.03441.54410.10980.0593-0.29790.22750.19380.17230.02410.0404-0.21210.19870.02170.04790.15040.04140.177623.57648.22027.3483
56.3447-0.3289-0.27920.62220.25744.45780.0999-0.32480.79970.7184-0.03230.0991-0.92790.1447-0.22960.3907-0.04190.09410.1729-0.04160.236727.222117.675815.4562
61.02080.22661.47682.5571.02042.33740.514-0.502-0.72060.0498-0.1447-0.8613-0.23722.5695-0.31660.33-0.1650.03930.8209-0.07520.767341.290211.713626.4125
71.6361-0.8563-2.57942.15570.80644.24170.6017-0.40430.20620.3280.06020.3687-0.4340.4267-0.39170.3094-0.10960.11010.3956-0.07440.252541.427315.091616.3192
81.2887-0.5716-1.74973.9802-0.24862.86590.1266-0.12-0.09540.047-0.1187-0.5822-0.09290.19040.03810.1496-0.0094-0.02590.19380.02620.171535.81422.98139.0468
96.6795-4.836-1.68274.55490.89350.5154-0.2476-1.4342-0.09850.39040.72690.3798-0.24020.2606-0.43180.39560.03060.08280.35920.01770.139622.974113.30321.6577
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 1:10)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 11:29)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 30:48)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 49:65)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 66:79)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 80:86)
7X-RAY DIFFRACTION7(CHAIN A AND RESID 87:96)
8X-RAY DIFFRACTION8(CHAIN A AND RESID 97:119)
9X-RAY DIFFRACTION9(CHAIN A AND RESID 120:135)

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