[English] 日本語
Yorodumi
- PDB-4z4v: Crystal structure of GII.10 P domain in complex with 19mM fucose -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4z4v
TitleCrystal structure of GII.10 P domain in complex with 19mM fucose
ComponentsCapsid proteinCapsid
KeywordsVIRAL PROTEIN / fucose / norovirus / protruding domain
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 / Picornavirus/Calicivirus coat protein / Viral coat protein subunit ...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 / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
beta-L-fucopyranose / NITRATE ION / Capsid protein
Similarity search - Component
Biological speciesNorovirus GII.10
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsKoromyslova, A.D. / Leuthold, M.M. / Hansman, G.S.
CitationJournal: Virology / Year: 2015
Title: The sweet quartet: Binding of fucose to the norovirus capsid.
Authors: Koromyslova, A.D. / Leuthold, M.M. / Bowler, M.W. / Hansman, G.S.
History
DepositionApr 2, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 27, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 3, 2015Group: Database references
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / diffrn_radiation_wavelength ...chem_comp / diffrn_radiation_wavelength / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Capsid protein
B: Capsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,73612
Polymers69,0132
Non-polymers72310
Water11,259625
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5890 Å2
ΔGint13 kcal/mol
Surface area23780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.109, 78.823, 68.656
Angle α, β, γ (deg.)90.000, 99.770, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: MET / End label comp-ID: MET / Auth seq-ID: 224 - 538 / Label seq-ID: 1 - 315

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain AAA
2chain BBB

-
Components

#1: Protein Capsid protein / Capsid


Mass: 34506.660 Da / Num. of mol.: 2 / Fragment: Protruding domain, UNP residues 224-538
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Norovirus GII.10 / Plasmid: pMBP / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q5F4T5
#2: Chemical ChemComp-NO3 / NITRATE ION / Nitrate


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#4: Sugar ChemComp-FUL / beta-L-fucopyranose / beta-L-fucose / 6-deoxy-beta-L-galactopyranose / L-fucose / fucose / 6-DEOXY-BETA-L-GALACTOSE / Fucose


Type: L-saccharide, beta linking / Mass: 164.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O5
IdentifierTypeProgram
LFucpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-L-fucopyranoseCOMMON NAMEGMML 1.0
b-L-FucpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
FucSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 625 / 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: 2.52 Å3/Da / Density % sol: 51.11 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: sodium nitrate, bis-tris propane, PEG3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.984463 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Feb 20, 2015
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.984463 Å / Relative weight: 1
ReflectionResolution: 1.799→43.05 Å / Num. obs: 62752 / % possible obs: 98.8 % / Redundancy: 2.9 % / Net I/σ(I): 16.73
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-IDRejects% possible all
1.799-1.8632.90.38163.021095.1
10
10

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation7.11 Å43.08 Å
Translation7.11 Å43.08 Å

-
Processing

Software
NameVersionClassification
PHASER2.5.6phasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ONU
Resolution: 1.8→43 Å / SU ML: 0.17 / Cross valid method: NONE / σ(F): 1.37 / Phase error: 17.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1794 3136 5 %
Rwork0.1483 59590 -
obs0.1498 62726 98.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 68.15 Å2 / Biso mean: 25.3622 Å2 / Biso min: 8.72 Å2
Refinement stepCycle: final / Resolution: 1.8→43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4736 0 47 625 5408
Biso mean--30.95 34.61 -
Num. residues----619
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114971
X-RAY DIFFRACTIONf_angle_d1.2886805
X-RAY DIFFRACTIONf_chiral_restr0.064762
X-RAY DIFFRACTIONf_plane_restr0.008900
X-RAY DIFFRACTIONf_dihedral_angle_d12.1471764
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2826X-RAY DIFFRACTION6.387TORSIONAL
12B2826X-RAY DIFFRACTION6.387TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 22

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.799-1.82710.28051290.21672446257591
1.8271-1.8570.24171420.20252698284099
1.857-1.8890.25761390.19372661280099
1.889-1.92340.19491430.19372726286999
1.9234-1.96040.24171430.18332704284799
1.9604-2.00040.22721420.1812711285399
2.0004-2.04390.20991450.16627402885100
2.0439-2.09140.23271430.16012721286499
2.0914-2.14380.19321420.152926952837100
2.1438-2.20170.22741430.158227262869100
2.2017-2.26650.18871440.151627312875100
2.2665-2.33960.15811430.148427172860100
2.3396-2.42330.18611440.141827262870100
2.4233-2.52030.18151410.14942697283899
2.5203-2.6350.20561450.15172750289599
2.635-2.77390.171440.15862722286699
2.7739-2.94760.18461430.15182717286099
2.9476-3.17510.16771440.15222734287899
3.1751-3.49450.16511430.14322721286499
3.4945-3.99990.15081430.13262727287099
3.9999-5.03820.13491450.10962749289499
5.0382-43.06750.15641460.13432771291798
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.5749-0.0806-0.13271.05620.19571.8056-0.00070.04990.047-0.06430.0069-0.0159-0.15280.0402-0.0160.1616-0.0101-0.0150.14790.00770.14658.57279.161911.7727
20.72460.0324-0.1411.0305-0.16271.3888-0.02710.06060.0583-0.06630.06110.0472-0.1209-0.0284-0.03380.1227-0.0035-0.00750.11190.00640.1074.01318.564413.3224
33.93691.2785-0.95291.5892-0.60773.3061-0.09090.1792-0.1942-0.27990.0653-0.14070.17560.25810.03220.27510.0020.03760.2181-0.03770.125815.464-3.7782-9.1496
42.01930.640.12711.5763-0.15750.73370.0478-0.0219-0.13060.0425-0.0111-0.11670.09460.0416-0.02750.14330.0046-0.01390.12060.00050.1317.6656-9.577222.6742
51.2513-0.28690.20621.1471-0.06530.7842-0.015-0.1387-0.14490.13080.0494-0.05510.0584-0.0074-0.03440.1352-0.0034-0.00690.11440.01450.110711.5582-8.912429.6125
62.49180.17440.38881.55310.78642.4590.06530.1761-0.0996-0.11840.1116-0.559-0.19340.3148-0.15470.155-0.01570.03730.2037-0.02710.307136.48090.854120.0549
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 224 through 341 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 342 through 472 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 473 through 538 )A0
4X-RAY DIFFRACTION4chain 'B' and (resid 224 through 327 )B0
5X-RAY DIFFRACTION5chain 'B' and (resid 328 through 455 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 456 through 538 )B0

+
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