[English] 日本語
Yorodumi
- PDB-6i3h: Crystal structure of influenza A virus M1 N-terminal domain (G18A... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6i3h
TitleCrystal structure of influenza A virus M1 N-terminal domain (G18A mutation)
ComponentsMatrix protein 1
KeywordsVIRAL PROTEIN / Matrix protein 1 N-terminal domain G18A mutation
Function / homology
Function and homology information


viral budding from plasma membrane / structural constituent of virion / host cell nucleus / virion membrane / RNA binding / membrane
Similarity search - Function
Influenza matrix protein M1, N-terminal subdomain 2 / Matrix protein 1 / Influenza matrix M1, N-terminal / Influenza matrix M1, C-terminal / Influenza matrix M1, N-terminal subdomain 1 / Influenza matrix M1, N-terminal subdomain 2 / Influenza virus matrix protein M1 / Influenza Matrix protein (M1) / Influenza Matrix protein (M1) C-terminal domain / Influenza Matrix protein (M1) C-terminal domain ...Influenza matrix protein M1, N-terminal subdomain 2 / Matrix protein 1 / Influenza matrix M1, N-terminal / Influenza matrix M1, C-terminal / Influenza matrix M1, N-terminal subdomain 1 / Influenza matrix M1, N-terminal subdomain 2 / Influenza virus matrix protein M1 / Influenza Matrix protein (M1) / Influenza Matrix protein (M1) C-terminal domain / Influenza Matrix protein (M1) C-terminal domain / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PHOSPHATE ION / Matrix protein 1
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsMiyake, Y. / Keusch, J.J. / Decamps, L. / Ho-Xuan, H. / Iketani, S. / Gut, H. / Kutay, U. / Helenius, A. / Yamauchi, Y.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Switzerland
CitationJournal: Nat Microbiol / Year: 2019
Title: Influenza virus uses transportin 1 for vRNP debundling during cell entry.
Authors: Miyake, Y. / Keusch, J.J. / Decamps, L. / Ho-Xuan, H. / Iketani, S. / Gut, H. / Kutay, U. / Helenius, A. / Yamauchi, Y.
History
DepositionNov 6, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 18, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Matrix protein 1
B: Matrix protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,2554
Polymers39,0652
Non-polymers1902
Water2,756153
1
A: Matrix protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6282
Polymers19,5331
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Matrix protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6282
Polymers19,5331
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.560, 35.580, 69.290
Angle α, β, γ (deg.)89.71, 84.40, 69.02
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein Matrix protein 1 / M1


Mass: 19532.600 Da / Num. of mol.: 2 / Mutation: G18A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Plasmid: pOPINF / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P05777
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / 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: 2.08 Å3/Da / Density % sol: 40.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 30% EDO_P8K, 0.1 M MB2 pH 7.5, 10% NPS

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 23546 / % possible obs: 94.6 % / Redundancy: 1.96 % / Biso Wilson estimate: 34.43 Å2 / CC1/2: 0.997 / Rsym value: 0.048 / Net I/σ(I): 9.69
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 1.95 % / Mean I/σ(I) obs: 2.15 / Num. unique obs: 1731 / CC1/2: 0.804 / Rsym value: 0.371 / % possible all: 93.6

-
Processing

Software
NameVersionClassification
BUSTER2.11.5refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CQE

5cqe


Resolution: 1.9→21.37 Å / Cor.coef. Fo:Fc: 0.9425 / Cor.coef. Fo:Fc free: 0.9347 / SU R Cruickshank DPI: 0.181 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.178 / SU Rfree Blow DPI: 0.149 / SU Rfree Cruickshank DPI: 0.151
RfactorNum. reflection% reflectionSelection details
Rfree0.2327 1177 5 %RANDOM
Rwork0.2059 ---
obs0.2072 23530 94.65 %-
Displacement parametersBiso mean: 44.44 Å2
Baniso -1Baniso -2Baniso -3
1-3.7845 Å21.0452 Å2-1.2921 Å2
2--3.1035 Å2-5.2663 Å2
3----6.888 Å2
Refine analyzeLuzzati coordinate error obs: 0.295 Å
Refinement stepCycle: 1 / Resolution: 1.9→21.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2512 0 10 153 2675
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012561HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.033467HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d904SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes58HARMONIC2
X-RAY DIFFRACTIONt_gen_planes369HARMONIC5
X-RAY DIFFRACTIONt_it2561HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.64
X-RAY DIFFRACTIONt_other_torsion18.31
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion340SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies4HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3180SEMIHARMONIC4
LS refinement shellResolution: 1.9→1.98 Å / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.241 145 5.02 %
Rwork0.2208 2742 -
all0.2217 2887 -
obs--94.65 %
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)
11.64971.17130.45165.6381-1.23411.59760.1064-0.1101-0.0198-0.1567-0.2717-0.7583-0.05840.09010.1653-0.1892-0.00340.0071-0.1310.02210.034816.953960.58166.3094
24.09251.1408-0.24832.14670.46331.0267-0.11650.01790.13780.01080.01590.45520.0956-0.03110.1006-0.17430.00060.0038-0.1521-0.06080.054434.829756.134834.4747
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

+
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