[English] 日本語
Yorodumi
- PDB-2jjl: Structure of avian reovirus sigmaC117-326, P321 crystal form -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2jjl
TitleStructure of avian reovirus sigmaC117-326, P321 crystal form
ComponentsSIGMA-C CAPSID PROTEIN
KeywordsVIRAL PROTEIN / ALPHA-HELICAL COILED COIL / RECEPTOR-BINDING / TRIPLE BETA-SPIRAL / VIRION / COILED COIL / BETA-BARREL
Function / homology
Function and homology information


viral capsid / symbiont entry into host cell / virion attachment to host cell
Similarity search - Function
Adenovirus Type 5 Fiber Protein (Receptor Binding Domain) - #40 / Reovirus sigma C capsid protein, C-terminal / Reovirus sigma C capsid protein triple beta spiral / Reovirus sigma C capsid protein C-terminal domain / Reovirus sigma C capsid protein triple beta spiral / reovirus attachment protein sigma1; domain 1 / Adenovirus Type 5 Fiber Protein (Receptor Binding Domain) / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #170 / Laminin / Single alpha-helices involved in coiled-coils or other helix-helix interfaces ...Adenovirus Type 5 Fiber Protein (Receptor Binding Domain) - #40 / Reovirus sigma C capsid protein, C-terminal / Reovirus sigma C capsid protein triple beta spiral / Reovirus sigma C capsid protein C-terminal domain / Reovirus sigma C capsid protein triple beta spiral / reovirus attachment protein sigma1; domain 1 / Adenovirus Type 5 Fiber Protein (Receptor Binding Domain) / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #170 / Laminin / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Ribbon / Up-down Bundle / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Sigma-C capsid protein
Similarity search - Component
Biological speciesAVIAN REOVIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsGuardado-Calvo, P. / Fox, G.C. / Llamas-Saiz, A.L. / Benavente, J. / van Raaij, M.J.
Citation
Journal: J. Gen. Virol. / Year: 2009
Title: Crystallographic structure of the alpha-helical triple coiled-coil domain of avian reovirus S1133 fibre.
Authors: Guardado-Calvo, P. / Fox, G.C. / Llamas-Saiz, A.L. / van Raaij, M.J.
#1: Journal: Acta Crystallogr., Sect.F / Year: 2005
Title: Crystallization of the C-Terminal Globular Domain of Avian Reovirus Fibre.
Authors: van Raaij, M.J. / Hermo-Parrado, X.L. / Guardado-Calvo, P. / Fox, G.C. / Llamas-Saiz, A.L. / Costas, C. / Martinez-Costas, J. / Benavente, J.
#2: Journal: J.Mol.Biol. / Year: 2005
Title: Structure of the Carboxy-Terminal Receptor-Binding Domain of Avian Reovirus Fibre Sigmac.
Authors: Guardado-Calvo, P. / Fox, G.C. / Hermo-Parrado, X.L. / Llamas-Saiz, A.L. / Costas, C. / Martinez-Costas, J. / Benavente, J. / van Raaij, M.J.
History
DepositionApr 14, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 13, 2009Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name
Revision 1.4Dec 13, 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 / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: SIGMA-C CAPSID PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9507
Polymers22,5871
Non-polymers3636
Water3,639202
1
A: SIGMA-C CAPSID PROTEIN
hetero molecules

A: SIGMA-C CAPSID PROTEIN
hetero molecules

A: SIGMA-C CAPSID PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,85121
Polymers67,7613
Non-polymers1,09018
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 area12620 Å2
ΔGint-100.8 kcal/mol
Surface area31650 Å2
MethodPQS
Unit cell
Length a, b, c (Å)77.657, 77.657, 121.449
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11A-1327-

CL

21A-1328-

CL

31A-1330-

ZN

41A-1331-

ZN

-
Components

#1: Protein SIGMA-C CAPSID PROTEIN / SIGMA-3 PROTEIN


Mass: 22587.023 Da / Num. of mol.: 1 / Fragment: RESIDUES 117-326
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) AVIAN REOVIRUS / Strain: S1133
Description: THE AVIAN REOVIRUS STRAIN S1133 WAS ORIGINALLY PROVIDED BY DR. PHILIP I.MARCUS WHEN DR. J.BENAVENTE WAS A ROCHE VISITING SCIENTIST IN THE LABORATORY OF DR. A.SHATKIN
Plasmid: PET28C-PLUS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): JM109 / Variant (production host): DE3 / References: UniProt: Q992I2
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 202 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE FIRST RESIDUE, ILE-116, IS A REMNANT OF THE EXPRESSION TAG.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 4.7 Å3/Da / Density % sol: 73.7 % / Description: NONE
Crystal growpH: 8.4
Details: 0.6-0.75 M AMMONIUM SULPHATE, 0.1 M TRIS-HCL PH 8.4, 25% GLYCEROL, 50 MM ZINC SULPHATE

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM16 / Wavelength: 0.984
DetectorType: ADSC CCD / Detector: CCD / Date: Oct 3, 2007 / Details: RD COATED FLAT AND TOROIDAL MIRRORS
RadiationMonochromator: SI111 DOUBLE-CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.984 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 19318 / % possible obs: 99 % / Redundancy: 20 % / Biso Wilson estimate: 44.1 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 52.6
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 20.3 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 10.4 / % possible all: 98.7

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: CHAIN C OF PDB ENTRY 2VRS

2vrs


Resolution: 2.3→25 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.94 / SU B: 3.7 / SU ML: 0.093 / Cross valid method: THROUGHOUT / ESU R: 0.175 / ESU R Free: 0.165 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.22 1514 7.9 %RANDOM
Rwork0.181 ---
obs0.184 17714 99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.49 Å2
Baniso -1Baniso -2Baniso -3
1-2.19 Å21.1 Å20 Å2
2--2.19 Å20 Å2
3----3.29 Å2
Refinement stepCycle: LAST / Resolution: 2.3→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1550 0 10 202 1762
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0211586
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5091.9462157
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4995206
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.86423.38565
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.09515243
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6441511
X-RAY DIFFRACTIONr_chiral_restr0.0990.2257
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021194
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1950.2594
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2950.21112
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1630.2126
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1830.280
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2140.214
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.22551056
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.85271666
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it7.17110594
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it8.86215491
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.46 Å / Total num. of bins used: 8 /
RfactorNum. reflection
Rfree0.301 268
Rwork0.216 3116

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more