[English] 日本語
Yorodumi
- PDB-4fpq: Structure of a fungal protein -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4fpq
TitleStructure of a fungal protein
ComponentsAvirulence Effector AvrLm4-7
KeywordsPROTEIN BINDING / alpha-beta protein / Aviraulence protein
Function / homologyAvirulence Effector AvrLm4-7 / Avirulence Effector AvrLm4-7 / Avirulence Effector AvrLm4-7 domain-containing protein
Function and homology information
Biological speciesLeptosphaeria maculans (blackleg of rapeseed fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsBlondeau, K. / Blaise, F. / Graille, M. / Linglin, J. / Ollivier, B. / Labarde, A. / Doizy, A. / Daverdin, G. / Balesdent, M.H. / Rouxel, T. ...Blondeau, K. / Blaise, F. / Graille, M. / Linglin, J. / Ollivier, B. / Labarde, A. / Doizy, A. / Daverdin, G. / Balesdent, M.H. / Rouxel, T. / van Tilbeurgh, H. / Fudal, I.
CitationJournal: Plant J. / Year: 2015
Title: Crystal structure of the effector AvrLm4-7 of Leptosphaeria maculans reveals insights into its translocation into plant cells and recognition by resistance proteins.
Authors: Blondeau, K. / Blaise, F. / Graille, M. / Kale, S.D. / Linglin, J. / Ollivier, B. / Labarde, A. / Lazar, N. / Daverdin, G. / Balesdent, M.H. / Choi, D.H. / Tyler, B.M. / Rouxel, T. / van ...Authors: Blondeau, K. / Blaise, F. / Graille, M. / Kale, S.D. / Linglin, J. / Ollivier, B. / Labarde, A. / Lazar, N. / Daverdin, G. / Balesdent, M.H. / Choi, D.H. / Tyler, B.M. / Rouxel, T. / van Tilbeurgh, H. / Fudal, I.
History
DepositionJun 22, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 1, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Revision 1.2Nov 12, 2025Group: Data collection / Refinement description / Structure summary
Category: audit_author / diffrn_radiation_wavelength ...audit_author / diffrn_radiation_wavelength / diffrn_source / software
Item: _audit_author.name / _diffrn_source.pdbx_wavelength_list / _software.classification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Avirulence Effector AvrLm4-7
B: Avirulence Effector AvrLm4-7
C: Avirulence Effector AvrLm4-7
D: Avirulence Effector AvrLm4-7


Theoretical massNumber of molelcules
Total (without water)59,5204
Polymers59,5204
Non-polymers00
Water3,603200
1
A: Avirulence Effector AvrLm4-7


Theoretical massNumber of molelcules
Total (without water)14,8801
Polymers14,8801
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Avirulence Effector AvrLm4-7


Theoretical massNumber of molelcules
Total (without water)14,8801
Polymers14,8801
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Avirulence Effector AvrLm4-7


Theoretical massNumber of molelcules
Total (without water)14,8801
Polymers14,8801
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Avirulence Effector AvrLm4-7


Theoretical massNumber of molelcules
Total (without water)14,8801
Polymers14,8801
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: Avirulence Effector AvrLm4-7
B: Avirulence Effector AvrLm4-7


Theoretical massNumber of molelcules
Total (without water)29,7602
Polymers29,7602
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1590 Å2
ΔGint-7 kcal/mol
Surface area14520 Å2
MethodPISA
6
C: Avirulence Effector AvrLm4-7
D: Avirulence Effector AvrLm4-7


Theoretical massNumber of molelcules
Total (without water)29,7602
Polymers29,7602
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1630 Å2
ΔGint-7 kcal/mol
Surface area14540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.830, 60.830, 155.110
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

-
Components

#1: Protein
Avirulence Effector AvrLm4-7


Mass: 14879.876 Da / Num. of mol.: 4 / Mutation: I80K, G120R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leptosphaeria maculans (blackleg of rapeseed fungus)
Strain: JN3 / isolate v23.1.3 / race Av1-4-5-6-7-8 / Gene: AvrLm4-7, LEMA_P086290.1 / Production host: Komagataella pastoris (fungus) / References: UniProt: E5A6Z5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 200 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.41 Å3/Da / Density % sol: 48.98 %
Crystal growTemperature: 292 K / Method: vapor diffusion / pH: 8
Details: 1.2M Na/K tartrate, 100 mM Tris pH8, VAPOR DIFFUSION, temperature 292K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 4, 2010
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. all: 25106 / Num. obs: 24177 / % possible obs: 96.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 13.6
Reflection shellResolution: 2.3→2.43 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.435 / Mean I/σ(I) obs: 3.6 / % possible all: 99.4

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
PHENIX(phenix.refine)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→28.315 Å / SU ML: 0.49 / σ(F): 1.99 / Phase error: 34.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3082 1202 5 %RANDOM
Rwork0.2436 ---
all0.25 24036 --
obs0.2468 24036 96.21 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 67.613 Å2 / ksol: 0.37 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-6.0767 Å20 Å2-0 Å2
2--6.0767 Å20 Å2
3----12.1534 Å2
Refinement stepCycle: LAST / Resolution: 2.3→28.315 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4066 0 0 200 4266
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084231
X-RAY DIFFRACTIONf_angle_d1.0835729
X-RAY DIFFRACTIONf_dihedral_angle_d16.5341525
X-RAY DIFFRACTIONf_chiral_restr0.074613
X-RAY DIFFRACTIONf_plane_restr0.005739
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3001-2.39210.31591370.24972629X-RAY DIFFRACTION100
2.3921-2.50090.34831380.24282616X-RAY DIFFRACTION100
2.5009-2.63270.40271390.26882632X-RAY DIFFRACTION100
2.6327-2.79750.44471230.3242345X-RAY DIFFRACTION89
2.7975-3.01330.37291390.26632635X-RAY DIFFRACTION100
3.0133-3.31610.29991390.24432627X-RAY DIFFRACTION100
3.3161-3.7950.35431230.25492352X-RAY DIFFRACTION89
3.795-4.77750.24551320.20382507X-RAY DIFFRACTION95
4.7775-28.31750.23351320.18572491X-RAY DIFFRACTION93

+
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