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- PDB-4jf3: Crystal structure of the mpmv tm retroviral fusion core -

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Basic information

Entry
Database: PDB / ID: 4jf3
TitleCrystal structure of the mpmv tm retroviral fusion core
ComponentsEnvelope glycoprotein
KeywordsVIRAL PROTEIN / six-helix bundle / fusion / MPMV TM / virus envelope
Function / homology
Function and homology information


fusion of virus membrane with host plasma membrane / viral envelope / symbiont entry into host cell / virion attachment to host cell / host cell plasma membrane / virion membrane / membrane
Similarity search - Function
ENV polyprotein (coat polyprotein) / TLV/ENV coat polyprotein / Helix Hairpins - #210 / Helix Hairpins / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Envelope glycoprotein
Similarity search - Component
Biological speciesMason-Pfizer monkey virus
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsCook, J.D. / Aydin, H. / Lee, J.E.
CitationJournal: J.Virol. / Year: 2014
Title: Crystal structures of Beta- and gammaretrovirus fusion proteins reveal a role for electrostatic stapling in viral entry.
Authors: Aydin, H. / Cook, J.D. / Lee, J.E.
History
DepositionFeb 27, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2014Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Envelope glycoprotein
B: Envelope glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9365
Polymers22,8302
Non-polymers1063
Water3,549197
1
A: Envelope glycoprotein
hetero molecules

A: Envelope glycoprotein
hetero molecules

A: Envelope glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4579
Polymers34,2443
Non-polymers2136
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area8820 Å2
ΔGint-117 kcal/mol
Surface area13470 Å2
MethodPISA
2
B: Envelope glycoprotein
hetero molecules

B: Envelope glycoprotein
hetero molecules

B: Envelope glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3516
Polymers34,2443
Non-polymers1063
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area8310 Å2
ΔGint-79 kcal/mol
Surface area13740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.951, 43.951, 81.732
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number143
Space group name H-MP3
Components on special symmetry positions
IDModelComponents
11A-601-

CL

21B-601-

CL

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Components

#1: Protein Envelope glycoprotein / Transmembrane protein / TM / Glycoprotein 20 / gp20


Mass: 11414.808 Da / Num. of mol.: 2 / Fragment: fusion core, UNP residues 412-513 / Mutation: C483S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mason-Pfizer monkey virus / Gene: env / Plasmid: pJexpress / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P07575
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 197 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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 Å3/Da / Density % sol: 38.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 18% (w/v) PEG 3400 and 0.2 M sodium thiocyanate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN A200 / Detector: CCD / Date: Feb 19, 2011
RadiationMonochromator: VariMax HF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→34.5 Å / Num. obs: 18731 / % possible obs: 96.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.41 % / Rmerge(I) obs: 0.046 / Χ2: 0.99 / Net I/σ(I): 19.3 / Scaling rejects: 1025
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2% possible all
1.7-1.764.10.3014.4697916941.2785.4
1.76-1.835.270.2755970118151.2395
1.83-1.915.490.2136.41039518711.1595.8
1.91-2.025.530.16481044518711.0596.4
2.02-2.145.560.12310.81038218530.9696.8
2.14-2.315.580.09214.21094619410.997.6
2.31-2.545.590.06818.91073419020.8798
2.54-2.915.610.04727.41088019210.8598.8
2.91-3.665.620.034391091619250.8899.2
3.66-34.55.580.02850.31093919380.9499.4

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Processing

Software
NameVersionClassificationNB
d*TREK9.9.8.9Ddata reduction
PHENIX1.8_1069refinement
PDB_EXTRACT3.11data extraction
CrystalCleardata collection
d*TREKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Y4M

1y4m


Resolution: 1.7→34.5 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.17 / σ(F): 2.01 / Phase error: 19.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1933 952 5.08 %random
Rwork0.1537 ---
all0.1556 ---
obs0.1556 18725 96.2 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 62.38 Å2 / Biso mean: 17.0525 Å2 / Biso min: 4.69 Å2
Refinement stepCycle: LAST / Resolution: 1.7→34.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1438 0 3 197 1638
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011446
X-RAY DIFFRACTIONf_angle_d1.1061942
X-RAY DIFFRACTIONf_chiral_restr0.072232
X-RAY DIFFRACTIONf_plane_restr0.004256
X-RAY DIFFRACTIONf_dihedral_angle_d17.701560
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7001-1.78970.2281220.22872314243688
1.7897-1.90190.20361360.18572544268095
1.9019-2.04870.20031310.17792520265196
2.0487-2.25480.19011380.13962579271797
2.2548-2.5810.18091470.14532600274798
2.581-3.25140.20041340.14872583271799
3.2514-34.51180.18931440.14882633277799
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)
10.54390.2079-0.16390.931-1.22923.90410.0313-0.0471-0.01970.06460.012-0.0265-0.04130.0863-0.04310.01450.0008-0.00880.0392-0.00260.08334.0497-0.6619-18.9426
22.26670.9931-2.20852.7852-3.08464.54250.0577-0.19-0.19180.1496-0.0903-0.03760.24560.33160.06020.1065-0.0082-0.02760.0811-0.02370.125211.0691-6.65760.4892
30.46430.16670.06960.84511.09393.73460.0187-0.0370.02930.07250.0070.03810.0199-0.0551-0.03220.02080.00090.00820.04060.00020.079417.937613.384522.494
41.98741.03232.13962.85873.26614.67280.0673-0.18660.14770.1202-0.11220.0223-0.2374-0.35890.06240.1015-0.01010.02870.08670.02150.129610.91219.343441.3563
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 423 through 488 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 489 through 512 )A0
3X-RAY DIFFRACTION3chain 'B' and (resid 421 through 488 )B0
4X-RAY DIFFRACTION4chain 'B' and (resid 489 through 512 )B0

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