[English] 日本語
Yorodumi
- PDB-4fbj: Structure of the Cif:Nedd8 complex - Photorhabdus luminescens Cyc... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4fbj
TitleStructure of the Cif:Nedd8 complex - Photorhabdus luminescens Cycle Inhibiting Factor in complex with human Nedd8
Components
  • Hypothetical protein
  • NEDD8
KeywordsCELL CYCLE/PROTEIN BINDING / Effector-Host target complex / Glutamine deamidase / Deamidation / BACTERIAL EFFECTOR / CELL CYCLE-PROTEIN BINDING complex
Function / homology
Function and homology information


symbiont-mediated perturbation of host cell cycle progression / protein-glutamine glutaminase / regulation of proteolysis / protein neddylation / TGF-beta receptor signaling activates SMADs / anatomical structure morphogenesis / Iron uptake and transport / protein modification process / modification-dependent protein catabolic process / protein localization ...symbiont-mediated perturbation of host cell cycle progression / protein-glutamine glutaminase / regulation of proteolysis / protein neddylation / TGF-beta receptor signaling activates SMADs / anatomical structure morphogenesis / Iron uptake and transport / protein modification process / modification-dependent protein catabolic process / protein localization / protein tag activity / UCH proteinases / Cargo recognition for clathrin-mediated endocytosis / Neddylation / toxin activity / ubiquitin-dependent protein catabolic process / hydrolase activity / host cell nucleus / ubiquitin protein ligase binding / regulation of transcription by RNA polymerase II / proteolysis / extracellular exosome / extracellular region / nucleoplasm / nucleus / cytosol
Similarity search - Function
Protein-glutamine deamidase Cif / Cycle inhibiting factor (CIF) / Nedd8-like ubiquitin / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin domain signature. / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues ...Protein-glutamine deamidase Cif / Cycle inhibiting factor (CIF) / Nedd8-like ubiquitin / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin domain signature. / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin-like domain / Ubiquitin domain profile. / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
NEDD8 / Protein-glutamine deamidase Cif
Similarity search - Component
Biological speciesPhotorhabdus luminescens subsp. laumondii (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsCrow, A. / Banfield, M.J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: The molecular basis of Nedd8 deamidation by the bacterial effector protein Cif
Authors: Crow, A. / Hughes, R.K. / Taieb, F. / Oswald, E. / Banfield, M.J.
History
DepositionMay 23, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 20, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: 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 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Hypothetical protein
B: NEDD8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,7173
Polymers39,6822
Non-polymers351
Water6,774376
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2800 Å2
ΔGint-20 kcal/mol
Surface area14660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.730, 56.090, 67.550
Angle α, β, γ (deg.)90.00, 104.13, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Hypothetical protein / / Cif


Mass: 29637.326 Da / Num. of mol.: 1 / Fragment: Effector domain, UNP residues 53-313 / Mutation: C123S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Photorhabdus luminescens subsp. laumondii (bacteria)
Strain: TT01 / Gene: plu2515 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q7N439
#2: Protein NEDD8 / / Neddylin / Neural precursor cell expressed developmentally down-regulated protein 8 / NEDD-8 / ...Neddylin / Neural precursor cell expressed developmentally down-regulated protein 8 / NEDD-8 / Ubiquitin-like protein Nedd8


Mass: 10044.623 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NEDD8 / Production host: Escherichia coli (E. coli) / Strain (production host): Rossetta (DE3) / References: UniProt: Q15843
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 376 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsTHE LIGAND IN THE STRUCTURE IS AN UNKNOWN ATOM OR ION WHICH MAY PROBABABLY BE AN CHLORIDE, AND WAS ...THE LIGAND IN THE STRUCTURE IS AN UNKNOWN ATOM OR ION WHICH MAY PROBABABLY BE AN CHLORIDE, AND WAS REFINED AS CL A 401.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.89 Å3/Da / Density % sol: 34.77 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.7
Details: 20% PEG 4000, 200mM sodium acetate, 100mM MES pH 6.7, VAPOR DIFFUSION, SITTING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9134 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 30, 2011
RadiationMonochromator: Double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9134 Å / Relative weight: 1
ReflectionResolution: 1.6→42.6 Å / Num. all: 39093 / Num. obs: 39093 / % possible obs: 96.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.4 % / Rsym value: 0.052 / Net I/σ(I): 11.5
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 4.3 % / Mean I/σ(I) obs: 3 / Rsym value: 0.288 / % possible all: 96.2

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 3GQJ and 1NDD

3gqj

1ndd


Resolution: 1.6→38.2 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.939 / SU B: 4.185 / SU ML: 0.078 / Cross valid method: THROUGHOUT / ESU R: 0.146 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23624 1881 5 %RANDOM
Rwork0.16485 ---
obs0.16848 35599 95.87 %-
all-39093 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.474 Å2
Baniso -1Baniso -2Baniso -3
1-0.21 Å20 Å2-0.43 Å2
2---0.46 Å20 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.6→38.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2586 0 1 376 2963
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0222829
X-RAY DIFFRACTIONr_angle_refined_deg2.0471.9773850
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8735366
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.81425.942138
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.65115551
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9831515
X-RAY DIFFRACTIONr_chiral_restr0.1430.2429
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212167
X-RAY DIFFRACTIONr_mcbond_it2.4131.51742
X-RAY DIFFRACTIONr_mcangle_it3.62822853
X-RAY DIFFRACTIONr_scbond_it5.33331087
X-RAY DIFFRACTIONr_scangle_it7.6424.5997
X-RAY DIFFRACTIONr_rigid_bond_restr2.82932417
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 120 -
Rwork0.263 2634 -
obs--95.36 %

+
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