[English] 日本語
Yorodumi
- PDB-4p25: Structure of the P domain from a GI.7 Norovirus variant in comple... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4p25
TitleStructure of the P domain from a GI.7 Norovirus variant in complex with LeY HBGA.
ComponentsMajor capsid protein
KeywordsVIRAL PROTEIN / P domain / Capsid protein / Norovirus / HBGA / LeY / Lewis HBGA
Function / homology
Function and homology information


Positive stranded ssRNA viruses / Nucleoplasmin-like/VP (viral coat and capsid proteins) / Positive stranded ssRNA viruses / Calicivirus coat protein C-terminal / Calicivirus coat protein C-terminal / Calicivirus coat protein / Calicivirus coat protein / Elongation Factor Tu (Ef-tu); domain 3 / Viral coat protein subunit / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Lewis Y antigen, beta anomer / Major capsid protein
Similarity search - Component
Biological speciesNorovirus Hu/GI.7/TCH-060/USA/2003
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.4991 Å
AuthorsShanker, S. / Czako, R. / Sankaran, B. / Atmar, R. / Estes, M. / Prasad, B.V.V.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK) United States
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: J.Virol. / Year: 2014
Title: Structural analysis of determinants of histo-blood group antigen binding specificity in genogroup I noroviruses.
Authors: Shanker, S. / Czako, R. / Sankaran, B. / Atmar, R.L. / Estes, M.K. / Prasad, B.V.
History
DepositionMar 1, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 2, 2014Provider: repository / Type: Initial release
Revision 1.1May 21, 2014Group: Database references
Revision 2.0Nov 27, 2019Group: Atomic model / Author supporting evidence ...Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Other / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / citation / entity / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_asym / struct_conn / struct_ref / struct_site_gen
Item: _atom_site.label_asym_id / _atom_site.label_entity_id ..._atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.type / _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_nonpoly_scheme.asym_id / _pdbx_nonpoly_scheme.entity_id / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ref.biol_id / _struct_site_gen.label_asym_id
Revision 3.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Refinement description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / refine_hist / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_value_order / _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_atom_id / _struct_conn.ptnr1_label_comp_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_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.1Dec 27, 2023Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Major capsid protein
B: Major capsid protein
C: Major capsid protein
D: Major capsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,4578
Polymers130,7544
Non-polymers2,7034
Water21,2221178
1
A: Major capsid protein
B: Major capsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,7284
Polymers65,3772
Non-polymers1,3512
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5570 Å2
ΔGint19 kcal/mol
Surface area22140 Å2
MethodPISA
2
C: Major capsid protein
D: Major capsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,7284
Polymers65,3772
Non-polymers1,3512
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5500 Å2
ΔGint17 kcal/mol
Surface area22640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.314, 63.124, 90.580
Angle α, β, γ (deg.)72.80, 82.18, 60.85
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein
Major capsid protein


Mass: 32688.531 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Norovirus Hu/GI.7/TCH-060/USA/2003 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: G8FL04
#2: Polysaccharide
alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2- ...alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose / Lewis Y antigen / beta anomer


Type: oligosaccharide, Oligosaccharide / Class: Antigen / Mass: 675.630 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with branches / References: Lewis Y antigen, beta anomer
DescriptorTypeProgram
LFucpa1-2DGalpb1-4[LFucpa1-3]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5][a2112h-1b_1-5]/1-2-3-2/a3-b1_a4-c1_c2-d1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-Galp]{[(2+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1178 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 45.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2M Sodium Formate 0.1M Bis Tris Propane 20% PEG3350

-
Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97939 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 17, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray / Wavelength: 0.97939 Å
Radiation wavelengthWavelength: 0.97939 Å / Relative weight: 1
ReflectionResolution: 1.499→40 Å / Num. obs: 176762 / % possible obs: 96.8 % / Redundancy: 3.9 % / Net I/σ(I): 28.5

-
Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.1_1168) / Classification: refinement
RefinementResolution: 1.4991→38.996 Å / SU ML: 0.13 / σ(F): 1.96 / Phase error: 17.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1745 8552 5.01 %
Rwork0.1342 --
obs0.1362 170635 92.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.4991→38.996 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8793 0 184 1178 10155
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0069244
X-RAY DIFFRACTIONf_angle_d1.16112669
X-RAY DIFFRACTIONf_dihedral_angle_d12.1323375
X-RAY DIFFRACTIONf_chiral_restr0.0711450
X-RAY DIFFRACTIONf_plane_restr0.0061648
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4991-1.51610.2411130.1542303X-RAY DIFFRACTION39
1.5161-1.53390.23241960.15443633X-RAY DIFFRACTION63
1.5339-1.55260.22582460.14564810X-RAY DIFFRACTION82
1.5526-1.57230.22013200.14135330X-RAY DIFFRACTION92
1.5723-1.5930.21672860.13165535X-RAY DIFFRACTION94
1.593-1.61480.20292890.12835528X-RAY DIFFRACTION95
1.6148-1.63790.19813260.12825530X-RAY DIFFRACTION95
1.6379-1.66230.20162800.12735578X-RAY DIFFRACTION95
1.6623-1.68830.19032880.12375600X-RAY DIFFRACTION95
1.6883-1.7160.19473080.12615605X-RAY DIFFRACTION96
1.716-1.74560.19743080.12065564X-RAY DIFFRACTION96
1.7456-1.77730.18123060.12075619X-RAY DIFFRACTION96
1.7773-1.81150.1862940.11195615X-RAY DIFFRACTION96
1.8115-1.84850.1822890.10915615X-RAY DIFFRACTION96
1.8485-1.88870.16653030.10985631X-RAY DIFFRACTION96
1.8887-1.93260.1812920.12015630X-RAY DIFFRACTION96
1.9326-1.98090.18283020.11345656X-RAY DIFFRACTION97
1.9809-2.03450.16572720.11455686X-RAY DIFFRACTION97
2.0345-2.09430.19772640.12425704X-RAY DIFFRACTION97
2.0943-2.16190.15622910.1175723X-RAY DIFFRACTION97
2.1619-2.23920.18283050.12015666X-RAY DIFFRACTION97
2.2392-2.32880.18342790.1285721X-RAY DIFFRACTION97
2.3288-2.43480.17373070.13145698X-RAY DIFFRACTION98
2.4348-2.56320.17442750.14135713X-RAY DIFFRACTION98
2.5632-2.72370.17723340.14365725X-RAY DIFFRACTION98
2.7237-2.9340.17073080.14335706X-RAY DIFFRACTION98
2.934-3.22910.15913010.14055647X-RAY DIFFRACTION97
3.2291-3.6960.1642970.13955441X-RAY DIFFRACTION93
3.696-4.65540.14652660.13745280X-RAY DIFFRACTION90
4.6554-39.00920.16493070.16975591X-RAY DIFFRACTION96

+
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