[English] 日本語
Yorodumi
- PDB-1ndd: STRUCTURE OF NEDD8 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ndd
TitleSTRUCTURE OF NEDD8
ComponentsPROTEIN (UBIQUITIN-LIKE PROTEIN NEDD8)
KeywordsSIGNALING PROTEIN / NEDD8 / NEDD-8 / UBIQUITIN-LIKE / PROTEOLYSIS
Function / homology
Function and homology information


protein neddylation / TGF-beta receptor signaling activates SMADs / regulation of proteolysis / regulation of postsynapse assembly / anatomical structure morphogenesis / Iron uptake and transport / modification-dependent protein catabolic process / protein modification process / protein tag activity / UCH proteinases ...protein neddylation / TGF-beta receptor signaling activates SMADs / regulation of proteolysis / regulation of postsynapse assembly / anatomical structure morphogenesis / Iron uptake and transport / modification-dependent protein catabolic process / protein modification process / protein tag activity / UCH proteinases / intracellular protein localization / Cargo recognition for clathrin-mediated endocytosis / Neddylation / ubiquitin-dependent protein catabolic process / postsynapse / ubiquitin protein ligase binding / regulation of transcription by RNA polymerase II / glutamatergic synapse / proteolysis / extracellular exosome / nucleoplasm / nucleus / cytoplasm / cytosol
Similarity search - Function
Nedd8-like ubiquitin / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. ...Nedd8-like ubiquitin / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Ubiquitin-like protein NEDD8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsWhitby, F.G. / Xia, G. / Pickart, C.M. / Hill, C.P.
CitationJournal: J.Biol.Chem. / Year: 1998
Title: Crystal structure of the human ubiquitin-like protein NEDD8 and interactions with ubiquitin pathway enzymes.
Authors: Whitby, F.G. / Xia, G. / Pickart, C.M. / Hill, C.P.
History
DepositionAug 21, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Feb 23, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 16, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: PROTEIN (UBIQUITIN-LIKE PROTEIN NEDD8)
B: PROTEIN (UBIQUITIN-LIKE PROTEIN NEDD8)
C: PROTEIN (UBIQUITIN-LIKE PROTEIN NEDD8)
D: PROTEIN (UBIQUITIN-LIKE PROTEIN NEDD8)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,75110
Polymers34,2964
Non-polymers4556
Water3,477193
1
A: PROTEIN (UBIQUITIN-LIKE PROTEIN NEDD8)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,6092
Polymers8,5741
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PROTEIN (UBIQUITIN-LIKE PROTEIN NEDD8)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,6092
Polymers8,5741
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: PROTEIN (UBIQUITIN-LIKE PROTEIN NEDD8)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,8624
Polymers8,5741
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: PROTEIN (UBIQUITIN-LIKE PROTEIN NEDD8)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,6702
Polymers8,5741
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5990 Å2
ΔGint-94 kcal/mol
Surface area13410 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)45.804, 64.972, 48.573
Angle α, β, γ (deg.)90.00, 96.66, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
PROTEIN (UBIQUITIN-LIKE PROTEIN NEDD8) / NEDD8


Mass: 8573.978 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: HUMAN NEDD8 UBIQUITIN-LIKE PROTEIN MONOMER WITH 4 MOLECULES IN THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT
Source: (gene. exp.) Homo sapiens (human) / Description: EXPRESSED IN E.COLI / Plasmid: PET3A-NEDD8 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLYSS / References: UniProt: Q15843
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 193 / 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: 2.1 Å3/Da / Density % sol: 41 %
Crystal growpH: 4.8 / Details: pH 4.8
Crystal
*PLUS
Density % sol: 41 %
Crystal grow
*PLUS
Temperature: 21 ℃ / pH: 7.6 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
240 mMTris1drop
350 mM1dropNaCl
40.4 mMEDTA1drop
50.2 mMdithiothreitol1drop
6100 mMcitric acid1reservoir
72.2 Mammonium sulfate1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MACSCIENCE / Detector: IMAGE PLATE / Details: MIRRORS
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→20 Å / Num. obs: 36579 / % possible obs: 97.8 % / Observed criterion σ(I): -2 / Redundancy: 6.9 % / Biso Wilson estimate: 21.1 Å2 / Rmerge(I) obs: 0.067 / Rsym value: 0.067 / Net I/σ(I): 20
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.452 / Mean I/σ(I) obs: 1.9 / Rsym value: 0.452 / % possible all: 93.7
Reflection
*PLUS
Num. measured all: 232354
Reflection shell
*PLUS
% possible obs: 93.7 %

-
Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.843refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1UBQ

1ubq


Resolution: 1.6→100 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.3 1109 3 %RANDOM
Rwork0.219 ---
obs0.219 36560 97.8 %-
Displacement parametersBiso mean: 23.2 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.23 Å
Luzzati sigma a0.22 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 1.6→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2349 0 22 193 2564
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.3
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.3
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.15
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 1.6→1.67 Å / Rfactor Rfree error: 0.036 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.46 163 3.7 %
Rwork0.428 4243 -
obs--94.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAMETER.ELEMENTSTOPOLOGY.ELEMENTS
X-RAY DIFFRACTION3SO4.PARSO4.TOP
X-RAY DIFFRACTION4PARAM19.IONTOPH19.ION
Software
*PLUS
Name: X-PLOR / Version: 3.843 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 100 Å / σ(F): 0 / % reflection Rfree: 3 % / Rfactor Rfree: 0.3
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 23.2 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.3
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.3
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.15
LS refinement shell
*PLUS
Rfactor Rfree: 0.46 / % reflection Rfree: 3.7 % / Rfactor Rwork: 0.428

+
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