[English] 日本語
Yorodumi
- PDB-6htl: Measles Phosphoprotein Coiled-Coil Domain IPKI Variant -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6htl
TitleMeasles Phosphoprotein Coiled-Coil Domain IPKI Variant
ComponentsPhosphoprotein
KeywordsVIRAL PROTEIN / Coiled-Coil / Alpha Helix / Tetramer / 3-10 Helix
Function / homology
Function and homology information


viral genome replication / RNA-dependent RNA polymerase activity / DNA-templated transcription / RNA binding / metal ion binding
Similarity search - Function
RNA polymerase, phosphoprotein P, C-terminal XD, paramyxovirinae / Paramyxovirus structural protein P/V, N-terminal domain / Paramyxovirus structural protein V/P N-terminus / P/V phosphoprotein, paramyxoviral / Paramyxovirus P/V phosphoprotein C-terminal / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #110 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesMeasles morbillivirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsSchramm, A. / Longhi, S.
CitationJournal: Sci Adv / Year: 2019
Title: Regulation of measles virus gene expression by P protein coiled-coil properties.
Authors: Bloyet, L.M. / Schramm, A. / Lazert, C. / Raynal, B. / Hologne, M. / Walker, O. / Longhi, S. / Gerlier, D.
History
DepositionOct 4, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 5, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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.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.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_symmetry

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Phosphoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,9662
Polymers8,9261
Non-polymers401
Water75742
1
A: Phosphoprotein
hetero molecules

A: Phosphoprotein
hetero molecules

A: Phosphoprotein
hetero molecules

A: Phosphoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8658
Polymers35,7044
Non-polymers1604
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area11590 Å2
ΔGint-134 kcal/mol
Surface area13570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.450, 33.450, 275.620
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422

-
Components

#1: Protein Phosphoprotein


Mass: 8926.093 Da / Num. of mol.: 1 / Mutation: L339I, L340P, L341K, L342I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Measles morbillivirus / Plasmid: pDest14 / Production host: Escherichia coli (E. coli) / References: UniProt: Q83623
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 42 / 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: 2.65 Å3/Da / Density % sol: 53.5 % / Description: elongated
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop / Details: PEG 4000, Calcium Chloride, Trizma / PH range: 8 - 9

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97911 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 30, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97911 Å / Relative weight: 1
ReflectionResolution: 2.2→45.94 Å / Num. obs: 4440 / % possible obs: 99.2 % / Redundancy: 22.3 % / Biso Wilson estimate: 35 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.016 / Rrim(I) all: 0.072 / Net I/σ(I): 15.8
Reflection shellResolution: 2.2→2.26 Å / Redundancy: 13.8 % / Rmerge(I) obs: 2.11 / Mean I/σ(I) obs: 1 / Num. unique obs: 287 / CC1/2: 0.956 / Rpim(I) all: 0.592 / Rrim(I) all: 2.202 / % possible all: 92.1

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
BUSTER2.10.3refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ZD0

3zd0


Resolution: 2.3→45.94 Å / Cor.coef. Fo:Fc: 0.907 / Cor.coef. Fo:Fc free: 0.885 / SU R Cruickshank DPI: 0.31 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.39 / SU Rfree Blow DPI: 0.26 / SU Rfree Cruickshank DPI: 0.239
Details: Even if collection were carried out at 2.2 angstrom resoltuion, the anisotropic nature of the data had a harmfull impact on model refinement especially when the 2.2 - 2.3 shell was included. ...Details: Even if collection were carried out at 2.2 angstrom resoltuion, the anisotropic nature of the data had a harmfull impact on model refinement especially when the 2.2 - 2.3 shell was included. Refinement was carried out at 2.3 angstrom as maximum resolution.
RfactorNum. reflection% reflectionSelection details
Rfree0.285 198 5.01 %RANDOM
Rwork0.252 ---
obs0.254 3952 99.9 %-
Displacement parametersBiso max: 112.32 Å2 / Biso mean: 30.44 Å2 / Biso min: 3 Å2
Baniso -1Baniso -2Baniso -3
1--1.7824 Å20 Å20 Å2
2---1.7824 Å20 Å2
3---3.5648 Å2
Refine analyzeLuzzati coordinate error obs: 0.45 Å
Refinement stepCycle: final / Resolution: 2.3→45.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms484 0 1 42 527
Biso mean--29.24 34.63 -
Num. residues----64
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d181SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes82HARMONIC5
X-RAY DIFFRACTIONt_it487HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion72SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact653SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d487HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg654HARMONIC21.13
X-RAY DIFFRACTIONt_omega_torsion2.24
X-RAY DIFFRACTIONt_other_torsion21.27
LS refinement shellResolution: 2.3→2.39 Å / Rfactor Rfree error: 0 / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.3728 22 5 %
Rwork0.3559 418 -
all0.3569 440 -
obs--99.32 %

+
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