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- PDB-1dyl: 9 ANGSTROM RESOLUTION CRYO-EM RECONSTRUCTION STRUCTURE OF SEMLIKI... -

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Basic information

Entry
Database: PDB / ID: 1dyl
Title9 ANGSTROM RESOLUTION CRYO-EM RECONSTRUCTION STRUCTURE OF SEMLIKI FOREST VIRUS (SFV) AND FITTING OF THE CAPSID PROTEIN STRUCTURE IN THE EM DENSITY
ComponentsNUCLEOCAPSID PROTEIN
KeywordsVIRUS/VIRAL PROTEIN / ALPHAVIRUS / SFV / CRYO-EM / IMAGE RECONSTRUCTION / ENVELOPED VIRUS / CAPSID PROTEIN / ICOSAHEDRAL VIRUS / VIRUS-VIRAL PROTEIN complex
Function / homology
Function and homology information


togavirin / T=4 icosahedral viral capsid / virion assembly / small molecule binding / host cell endosome / symbiont-mediated suppression of host toll-like receptor signaling pathway / clathrin-dependent endocytosis of virus by host cell / viral translational frameshifting / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane ...togavirin / T=4 icosahedral viral capsid / virion assembly / small molecule binding / host cell endosome / symbiont-mediated suppression of host toll-like receptor signaling pathway / clathrin-dependent endocytosis of virus by host cell / viral translational frameshifting / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / viral envelope / host cell nucleus / virion attachment to host cell / host cell plasma membrane / structural molecule activity / virion membrane / proteolysis / RNA binding / membrane
Similarity search - Function
Alphavirus E2 glycoprotein, domain B / Peptidase S3, togavirin / Alphavirus E2 glycoprotein / Alphavirus E3 spike glycoprotein / Alphavirus E1 glycoprotein / Alphavirus E2 glycoprotein, domain A / Alphavirus E2 glycoprotein, domain C / Alphavirus E2 glycoprotein / Alphavirus core protein / Alphavirus E3 glycoprotein ...Alphavirus E2 glycoprotein, domain B / Peptidase S3, togavirin / Alphavirus E2 glycoprotein / Alphavirus E3 spike glycoprotein / Alphavirus E1 glycoprotein / Alphavirus E2 glycoprotein, domain A / Alphavirus E2 glycoprotein, domain C / Alphavirus E2 glycoprotein / Alphavirus core protein / Alphavirus E3 glycoprotein / Alphavirus E1 glycoprotein / Alphavirus core protein (CP) domain profile. / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Flavivirus glycoprotein, central and dimerisation domain superfamily / Flaviviral glycoprotein E, dimerisation domain / Immunoglobulin E-set / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
Structural polyprotein
Similarity search - Component
Biological speciesSEMLIKI FOREST VIRUS
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 9 Å
AuthorsMancini, E.J. / Clarke, M. / Gowen, B.E. / Rutten, T. / Fuller, S.D.
CitationJournal: Mol Cell / Year: 2000
Title: Cryo-electron microscopy reveals the functional organization of an enveloped virus, Semliki Forest virus.
Authors: E J Mancini / M Clarke / B E Gowen / T Rutten / S D Fuller /
Abstract: Semliki Forest virus serves as a paradigm for membrane fusion and assembly. Our icosahedral reconstruction combined 5276 particle images from 48 cryo-electron micrographs and determined the virion ...Semliki Forest virus serves as a paradigm for membrane fusion and assembly. Our icosahedral reconstruction combined 5276 particle images from 48 cryo-electron micrographs and determined the virion structure to 9 A resolution. The improved resolution of this map reveals an N-terminal arm linking capsid subunits and defines the spike-capsid interaction sites. It illustrates the paired helical nature of the transmembrane segments and the elongated structures connecting them to the spike projecting domains. A 10 A diameter density in the fusion protein lines the cavity at the center of the spike. These clearly visible features combine with the variation in order between the layers to provide a framework for understanding the structural changes during the life cycle of an enveloped virus.
History
DepositionFeb 2, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 18, 2000Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 30, 2017Group: Data collection / Experimental preparation / Refinement description
Category: em_3d_fitting / em_sample_support / em_software
Item: _em_3d_fitting.target_criteria / _em_sample_support.grid_material ..._em_3d_fitting.target_criteria / _em_sample_support.grid_material / _em_sample_support.grid_mesh_size / _em_software.fitting_id / _em_software.image_processing_id / _em_software.name
Revision 1.4Jan 31, 2018Group: Data processing / Other / Category: cell / em_software
Item: _cell.Z_PDB / _cell.length_a ..._cell.Z_PDB / _cell.length_a / _cell.length_b / _cell.length_c / _em_software.details / _em_software.name
Revision 1.5Dec 18, 2019Group: Other / Category: atom_sites
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3]
Revision 1.6Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _pdbx_entry_details.has_protein_modification / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS [A,B,C,D]C IN EACH CHAIN ON SHEET RECORDS ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS [A,B,C,D]C IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Movie
  • Biological unit as complete icosahedral assembly
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  • Biological unit as icosahedral pentamer
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  • Biological unit as icosahedral 23 hexamer
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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
  • EMDB-1015
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  • Superimposition on EM map
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Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NUCLEOCAPSID PROTEIN
B: NUCLEOCAPSID PROTEIN
C: NUCLEOCAPSID PROTEIN
D: NUCLEOCAPSID PROTEIN


Theoretical massNumber of molelcules
Total (without water)65,0104
Polymers65,0104
Non-polymers00
Water00
1
A: NUCLEOCAPSID PROTEIN
B: NUCLEOCAPSID PROTEIN
C: NUCLEOCAPSID PROTEIN
D: NUCLEOCAPSID PROTEIN
x 60


Theoretical massNumber of molelcules
Total (without water)3,900,585240
Polymers3,900,585240
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: NUCLEOCAPSID PROTEIN
B: NUCLEOCAPSID PROTEIN
C: NUCLEOCAPSID PROTEIN
D: NUCLEOCAPSID PROTEIN
x 5


  • icosahedral pentamer
  • 325 kDa, 20 polymers
Theoretical massNumber of molelcules
Total (without water)325,04920
Polymers325,04920
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: NUCLEOCAPSID PROTEIN
B: NUCLEOCAPSID PROTEIN
C: NUCLEOCAPSID PROTEIN
D: NUCLEOCAPSID PROTEIN
x 6


  • icosahedral 23 hexamer
  • 390 kDa, 24 polymers
Theoretical massNumber of molelcules
Total (without water)390,05924
Polymers390,05924
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

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Components

#1: Protein
NUCLEOCAPSID PROTEIN


Mass: 16252.439 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) SEMLIKI FOREST VIRUS / Cell line: BABY HAMSTER KIDNEY 21 / Cellular location: EXTRACELLULAR / References: UniProt: P03315
Has protein modificationY
Sequence detailsTHE STRUCTURE STUDIED IS FOR THE COMPLETE VIRUS. THE FOLLOWING RESIDUES AND CHAINS ARE NOT REPORTED ...THE STRUCTURE STUDIED IS FOR THE COMPLETE VIRUS. THE FOLLOWING RESIDUES AND CHAINS ARE NOT REPORTED IN THIS ENTRY: MET A 1 TO ASP A 118 SER A 268 TO ARG A 1253 MET B 1 TO ASP B 118 SER B 268 TO ARG B 1253 MET C 1 TO ASP C 118 SER C 268 TO ARG C 1253 MET D 1 TO ASP D 118 SER D 268 TO ARG D 1253 AND CHAINS FOR THE SPIKE GLYCOPROTEINS E3, E2 AND E1

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: SEMLIKI FOREST VIRUS / Type: VIRUS
Buffer solutionpH: 7.6
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: 400 MESH COPPER, HOLEY CARBON, GLOW DISCHARGE, / Grid material: COPPER / Grid mesh size: 400 divisions/in.
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE
Details: PLUNGE VITRIFICATION SAMPLES PREPARED AS THIN LAYERS OF VITREOUS ICE MAINTAINED AT NEAR LIQUID NITROGEN TEMPERATURE IN THE ELECTRON MICROSCOPE WITH A GATAN 626-0300 CRYOTRANSFER HOLDER.
Crystal grow
*PLUS
Method: other / Details: Fuller, S.D., (1987) Cell. 48, 923.

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Electron microscopy imaging

MicroscopyModel: FEI/PHILIPS CM200FEG / Date: Jun 15, 1998
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal magnification: 50000 X / Nominal defocus max: 7600 nm / Nominal defocus min: 975 nm / Cs: 2 mm
Specimen holderTemperature: 95 K / Tilt angle max: 0 ° / Tilt angle min: 0 °
Image recordingElectron dose: 10 e/Å2 / Film or detector model: KODAK SO-163 FILM
Image scansNum. digital images: 48
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameCategory
1EMfitmodel fitting
2MRC IMAGE PROCESSING PACKAGEparticle selection
3SPIDERparticle selection
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionMethod: MODEL-BASED, POLAR-FOURIER- TRANSFORMATION (FULLER ET AL. 1996, J.STRUC.BIOL. 116, 48-55; BAKER AND CHENG 1996, J.STRUC.BIOL. 116, 120- 130) MODEL-BASED CROSS COMMOM LINES SEARCH AND ...Method: MODEL-BASED, POLAR-FOURIER- TRANSFORMATION (FULLER ET AL. 1996, J.STRUC.BIOL. 116, 48-55; BAKER AND CHENG 1996, J.STRUC.BIOL. 116, 120- 130) MODEL-BASED CROSS COMMOM LINES SEARCH AND REFINEMENT (CROWTHER ET AL. 1970, NATURE (LONDON) 226, 421- 425; FULLER ET AL. 1996, J.STRUC.BIOL. 11 48-55;FERLENGHI ET AL. 1998, J.MOL.BIOL. 283, 71-81)
Resolution: 9 Å / Num. of particles: 5267 / Nominal pixel size: 2.64 Å / Actual pixel size: 2.52 Å
Magnification calibration: THE PIXEL SIZE OF THE CRYO-EM MAP WAS CALIBRATED AGAINST A LOW RESOLUTION DENSITY MAP CALCULATED FROM THE CRYSTAL STRUCTURE OF HRV16. DENSITIES WERE COMPARED BY CROSS- ...Magnification calibration: THE PIXEL SIZE OF THE CRYO-EM MAP WAS CALIBRATED AGAINST A LOW RESOLUTION DENSITY MAP CALCULATED FROM THE CRYSTAL STRUCTURE OF HRV16. DENSITIES WERE COMPARED BY CROSS- CORRELATION WITHIN A SPHERICAL SHELL OF INTERNAL RADIUS 110 ANGSTROMS AND EXTERNAL RADIUS OF 145 ANGSTROMS.
Details: THE ORIENTATIONS WERE REFINED BY THE CROSS COMMON LINES LINES METHOD (SIMPLEX) AND THE POLAR FOURIER TRANSFORM METHOD USING A PARALLEL IMPLEMENTATION (PYPFT). THE EFFECTIVE RESOLUTION OF THE ...Details: THE ORIENTATIONS WERE REFINED BY THE CROSS COMMON LINES LINES METHOD (SIMPLEX) AND THE POLAR FOURIER TRANSFORM METHOD USING A PARALLEL IMPLEMENTATION (PYPFT). THE EFFECTIVE RESOLUTION OF THE FINAL RECONSTRUCTED DENSITY WAS DETERMINED TO BE AT LEAST 9 ANGSTROMS, AS MEASURED BY RANDOMLY SPLITTING THE PARTICLES INTO TWO SETS AND CALCULATING THE FOURIER SHELL CORRELATION OBTAINED FROM SEPARATE RECONSTRUCTIONS (HARAUZ AND VAN HEEL 1986, OPTIK 73, 146-156). THE EIGENVALUE SPECTRUM GAVE AN INDICATION OF THE RANDOMNESS OF THE DATA THAT WAS INCLUDED IN THE RECONSTRUCTION. THE COMPLETENESS OF THE DATA WAS VERIFIED IN THAT ALL EIGENVALUES EXCEEDED 100. THE COORDINATES ARE IN THE P, Q, R FRAME IN ANGSTROM UNITS AND CORRESPOND TO ICOSAHEDRAL SYMMETRY AXES. THE ORIGIN IS CHOSEN AT THE CENTER OF THE VIRUS WITH P, Q AND R ALONG MUTUALLY PERPENDICULAR TWO-FOLD AXES OF THE ICOSAHEDRON. THEY SHOULD REMAIN IN THAT FRAME FOR THE EASE OF THE USER IN CREATING THE BIOLOGICALLY SIGNIFICANT VIRAL COMPLEX PARTICLE USING THE 60 ICOSAHEDRAL SYMMETRY OPERATORS. RESIDUES NOT VISIBLE IN THE ORIGINAL CRYSTAL STRUCTURES ARE NOT INCLUDED IN THE CRYO-EM STRUCTURE MODEL. FOR EXAMPLE, C RESIDUES 1-118, ARE NOT VISIBLE IN THE CRYSTAL STRUCTURE (PDB ENTRY 1VCQ) AND THEREFORE ARE NOT INCLUDED IN THE COORDINATES BELOW.
Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL / Target criteria: R-factor
Details: METHOD--THE CRYSTAL STRUCTURE OF THE CAPSID PROTEIN FROM CHOI ET AL (1997) PROTEINS 3 27,345-359 (SUBUNIT A OF PDB FILE 1VCQ) WAS PLACED INTO THE CRYO-EM DENSITY MAP. THE CAPSID PROTEIN WAS ...Details: METHOD--THE CRYSTAL STRUCTURE OF THE CAPSID PROTEIN FROM CHOI ET AL (1997) PROTEINS 3 27,345-359 (SUBUNIT A OF PDB FILE 1VCQ) WAS PLACED INTO THE CRYO-EM DENSITY MAP. THE CAPSID PROTEIN WAS FIRST MANUALLY POSITIONED INTO THE CRYO-EM DENSITY CORRESPONDING TO POSITIONS OF THE FOUR INDEPENDENT MONOMER DENSITIES BETWEEN THE INNER LEAFLET OF THE BILAYER AND THE RNA. THESE POSITIONS WERE THEN REFINED BY RIGID BODY REFINEMENT IN REAL SPACE WITH THE PROGRAM EMFIT (CHENG ET AL. 1995, CELL 80, 621-630). THE QUALITY OF THE FIT CAN BE SEEN FROM THE MAP DENSITY WITHIN THE PROTEIN. ALL 4563 ATOMS ARE IN DENSITY OF AT LEAST 4 SIGMA (96.73) ABOVE THE AVERAGE (512.04) , 1167 ATOMS ARE IN DENSITY BETWEEN 4 AND 5 SIGMA, 3174 ATOMS ARE IN DENSITY BETWEEN 5 AND 6 SIGMA, AND 222 ATOMS ARE IN DENSTY OF 6 SIGMA OR ABOVE. THE VARIATION IN DENSITY OVER THE FITTED PROTEIN CAN BE VISUALIZED WITH THE PSEUDO TEMPERATURE FACTOR. THE DENSITY VALUE AT EACH ATOM IS GIVEN IN THE 8TH COLUM (USUALLY THE OCCUPANCY) AS THE NUMBER OF STANDARD DEVIATION ABOVE BACKGROUND. COLUMN NINE (USUALLY THE TEMPERATURE FACTOR) CONTAINS THE VALUE OF THE RELATIVE DENSITY WITHIN THE FITTED PROTEIN SCALED LINEARLY SO THAT THE MINIMUM DENSITY IS 100.0 AND THE MAXIMUM DENSITY IS 1.0. THE ATOMS THAT LIE IN THE LOWER DENSITY REGIONS WILL HAVE THE HIGHEST PSEUDO TEMPERATURE FACTORS. REFINEMENT PROTOCOL--RIGID BODY REFINEMENT
Atomic model buildingPDB-ID: 1DYL

Accession code: 1DYL / Source name: PDB / Type: experimental model
RefinementHighest resolution: 9 Å
Refinement stepCycle: LAST / Highest resolution: 9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4563 0 0 0 4563

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