[English] 日本語
Yorodumi
- PDB-4hbo: Crystal Structure of Rubella virus capsid protein (residues 127-277) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4hbo
TitleCrystal Structure of Rubella virus capsid protein (residues 127-277)
ComponentsCapsid protein
KeywordsVIRAL PROTEIN / partial beta barrel / capsid protein
Function / homology
Function and homology information


T=4 icosahedral viral capsid / host cell Golgi membrane / host cell mitochondrion / viral nucleocapsid / clathrin-dependent endocytosis of virus by host cell / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / virion membrane / RNA binding ...T=4 icosahedral viral capsid / host cell Golgi membrane / host cell mitochondrion / viral nucleocapsid / clathrin-dependent endocytosis of virus by host cell / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / virion membrane / RNA binding / metal ion binding / membrane
Similarity search - Function
Rubella virus capsid protein / Rubella capsid / Rubella membrane glycoprotein E1 / Rubella membrane glycoprotein E2 / Rubella membrane glycoprotein E1, domain 2 / Rubella membrane glycoprotein E1, domain 3 / Rubella membrane glycoprotein E1, domain 1 / Rubella capsid domain superfamily / Rubella membrane glycoprotein E1 / Rubella membrane glycoprotein E2 ...Rubella virus capsid protein / Rubella capsid / Rubella membrane glycoprotein E1 / Rubella membrane glycoprotein E2 / Rubella membrane glycoprotein E1, domain 2 / Rubella membrane glycoprotein E1, domain 3 / Rubella membrane glycoprotein E1, domain 1 / Rubella capsid domain superfamily / Rubella membrane glycoprotein E1 / Rubella membrane glycoprotein E2 / Rubella capsid protein / Chitinase A; domain 3 / Roll / Alpha Beta
Similarity search - Domain/homology
Structural polyprotein / Polyprotein
Similarity search - Component
Biological speciesRubella virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.241 Å
AuthorsMangala Prasad, V. / Fokine, A. / Rossmann, M.G.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Rubella virus capsid protein structure and its role in virus assembly and infection.
Authors: Mangala Prasad, V. / Willows, S.D. / Fokine, A. / Battisti, A.J. / Sun, S. / Plevka, P. / Hobman, T.C. / Rossmann, M.G.
History
DepositionSep 28, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2013Group: 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_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Revision 1.3Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Capsid protein
B: Capsid protein
C: Capsid protein
D: Capsid protein
E: Capsid protein


Theoretical massNumber of molelcules
Total (without water)74,9375
Polymers74,9375
Non-polymers00
Water00
1
A: Capsid protein

A: Capsid protein


Theoretical massNumber of molelcules
Total (without water)29,9752
Polymers29,9752
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455-x-1,y,-z+1/21
Buried area3210 Å2
ΔGint-28 kcal/mol
Surface area9030 Å2
MethodPISA
2
B: Capsid protein

B: Capsid protein


Theoretical massNumber of molelcules
Total (without water)29,9752
Polymers29,9752
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_454-x-1,y,-z-1/21
Buried area3180 Å2
ΔGint-23 kcal/mol
Surface area8560 Å2
MethodPISA
3
C: Capsid protein

C: Capsid protein


Theoretical massNumber of molelcules
Total (without water)29,9752
Polymers29,9752
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area4020 Å2
ΔGint-27 kcal/mol
Surface area9210 Å2
MethodPISA
4
D: Capsid protein

D: Capsid protein


Theoretical massNumber of molelcules
Total (without water)29,9752
Polymers29,9752
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area4210 Å2
ΔGint-34 kcal/mol
Surface area8540 Å2
MethodPISA
5
E: Capsid protein

E: Capsid protein


Theoretical massNumber of molelcules
Total (without water)29,9752
Polymers29,9752
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area3970 Å2
ΔGint-32 kcal/mol
Surface area8530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.790, 279.700, 76.725
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
DetailsThe biological unit is a dimer. There are 5 monomers in the asymmetric unit (chain A, B, C, D and E), which form 5 biological units on application of a 2-fold along 'b' axis.

-
Components

#1: Protein
Capsid protein


Mass: 14987.403 Da / Num. of mol.: 5 / Fragment: C-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rubella virus / Strain: M33 / Gene: Capsid / Plasmid: pGEX-KG / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8QL55, UniProt: P08563*PLUS
Has protein modificationY
Sequence detailsN-TERMINAL 20 AMINO ACIDS ASN PRO PHE GLN ALA ALA VAL ALA ARG GLY LEU ARG PRO PRO LEU HIS ASP PRO ...N-TERMINAL 20 AMINO ACIDS ASN PRO PHE GLN ALA ALA VAL ALA ARG GLY LEU ARG PRO PRO LEU HIS ASP PRO ASP THR WERE INCLUDED IN CRYSTALLIZATION SET UP BUT WERE DEGRADED DURING CRYSTALLIZATION

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.53 Å3/Da / Density % sol: 19.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 18% PEG 4000, 20% 2-propanol, 0.1 M Tris, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 20, 2011
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.241→50 Å / Num. obs: 7669 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.7 % / Rmerge(I) obs: 0.107 / Χ2: 1.351 / Net I/σ(I): 7.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
3.25-3.3110.80.5223571.198192.7
3.31-3.3712.70.4323671.2381100
3.37-3.4312.70.3153661.1631100
3.43-3.5120.2853901.2461100
3.5-3.5812.60.2633571.257194.2
3.58-3.6612.60.2623811.373199.5
3.66-3.7512.60.183671.3091100
3.75-3.8512.10.2413921.327199.7
3.85-3.9712.70.1823601.27196.5
3.97-4.0912.60.1493721.3331100
4.09-4.2412.20.123811.341199.7
4.24-4.4112.40.0983891.349199
4.41-4.6112.70.0993751.3941100
4.61-4.8512.80.0983921.394199.5
4.85-5.1613.50.093801.3991100
5.16-5.5613.60.0923991.351100
5.56-6.1114.10.0853961.2551100
6.11-713.90.0943941.4121100
7-8.8113.60.0734141.5661100
8.81-5012.30.0614401.712199.1

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.5 Å46.62 Å
Translation3.5 Å46.62 Å

-
Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASER2.3.0phasing
PHENIX1.8_1069refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4HAR

4har


Resolution: 3.241→46.617 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.5829 / SU ML: 0.44 / σ(F): 1.4 / Phase error: 44.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3679 1355 9.9 %Thin resolution shells
Rwork0.3398 ---
all0.3424 13688 --
obs0.3424 13688 96.69 %-
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 338.52 Å2 / Biso mean: 96.507 Å2 / Biso min: 20 Å2
Refinement stepCycle: LAST / Resolution: 3.241→46.617 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3155 0 0 0 3155
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073250
X-RAY DIFFRACTIONf_angle_d1.1974418
X-RAY DIFFRACTIONf_chiral_restr0.084437
X-RAY DIFFRACTIONf_plane_restr0.008586
X-RAY DIFFRACTIONf_dihedral_angle_d16.3951144
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.2408-3.35660.41011450.39851171131693
3.3566-3.4910.35581410.32681278141999
3.491-3.64980.40281450.34591234137997
3.6498-3.84210.3841370.32571266140399
3.8421-4.08270.39051410.33631204134598
4.0827-4.39770.28471320.28971277140999
4.3977-4.83990.31521340.29051264139899
4.8399-5.53920.33721390.31711260139999
5.5392-6.97510.44251320.3741261139399
6.9751-46.62150.42711090.44991118122786
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)
11.77790.8809-0.14860.59510.19631.3591-0.047-0.6216-1.0584-0.07240.0406-0.77430.4745-0.15850.11821.0564-0.02970.16780.669-0.17042.1687-16.404823.233815.1755
22.716-0.79131.67784.4382-0.14643.9173-0.1033-0.65731.78680.5965-0.2131-0.596-0.3035-0.45460.11940.47830.05690.03520.6204-0.24881.2492-15.944432.8537-14.6615
34.7848-1.5601-0.56533.4818-1.19164.37690.1229-0.2285-0.16940.0776-0.1026-0.85060.25850.82930.27920.8673-0.0484-0.28130.5017-0.00790.98494.442460.8908-16.0054
45.58481.9811.28794.8428-0.09313.8995-0.37860.5576-0.50860.1738-0.1669-0.24760.2854-0.30680.52090.50360.18420.06050.5088-0.08480.42554.485150.286415.2703
56.0551-1.672-0.28544.79560.15353.4745-0.1341-0.4219-0.83990.8732-0.3762-0.70330.23270.4490.50890.3624-0.02880.07260.60490.12230.57114.63545.817-14.9094
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and ((resseq 27:120))A27 - 120
2X-RAY DIFFRACTION2chain 'B' and ((resseq 27:120))B27 - 120
3X-RAY DIFFRACTION3chain 'C' and ((resseq 27:120))C27 - 120
4X-RAY DIFFRACTION4chain 'D' and ((resseq 27:120))D27 - 120
5X-RAY DIFFRACTION5chain 'E' and ((resseq 27:120))E27 - 120

+
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