[English] 日本語
Yorodumi
- PDB-3dqv: Structural Insights into NEDD8 Activation of Cullin-RING Ligases:... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3dqv
TitleStructural Insights into NEDD8 Activation of Cullin-RING Ligases: Conformational Control of Conjugation
Components
  • Cullin-5
  • NEDD8
  • Rbx1
KeywordsLIGASE / ubiquitin / nedd8 / scf / cullin-ring ligase / cullin / Nucleus / Ubl conjugation pathway / Host-virus interaction / Receptor / Ubl conjugation / Acetylation / Cytoplasm / DNA damage / DNA repair / Metal-binding / Zinc / Zinc-finger / SIGNALING PROTEIN
Function / homology
Function and homology information


ERBB2 signaling pathway / cullin-RING-type E3 NEDD8 transferase / cellular response to chemical stress / NEDD8 transferase activity / cullin-RING ubiquitin ligase complex / Cul7-RING ubiquitin ligase complex / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / regulation of proteolysis / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / positive regulation of protein autoubiquitination ...ERBB2 signaling pathway / cullin-RING-type E3 NEDD8 transferase / cellular response to chemical stress / NEDD8 transferase activity / cullin-RING ubiquitin ligase complex / Cul7-RING ubiquitin ligase complex / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / regulation of proteolysis / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / positive regulation of protein autoubiquitination / protein neddylation / NEDD8 ligase activity / Cul5-RING ubiquitin ligase complex / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / ubiquitin-ubiquitin ligase activity / Cul4A-RING E3 ubiquitin ligase complex / Cul2-RING ubiquitin ligase complex / SCF ubiquitin ligase complex / negative regulation of type I interferon production / Cul4B-RING E3 ubiquitin ligase complex / Cul3-RING ubiquitin ligase complex / Prolactin receptor signaling / protein monoubiquitination / TGF-beta receptor signaling activates SMADs / site of DNA damage / cullin family protein binding / anatomical structure morphogenesis / protein K48-linked ubiquitination / Nuclear events stimulated by ALK signaling in cancer / positive regulation of TORC1 signaling / Regulation of BACH1 activity / T cell activation / post-translational protein modification / intrinsic apoptotic signaling pathway / Degradation of DVL / Recognition of DNA damage by PCNA-containing replication complex / cellular response to amino acid stimulus / Degradation of GLI1 by the proteasome / Negative regulation of NOTCH4 signaling / Iron uptake and transport / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Vif-mediated degradation of APOBEC3G / Hedgehog 'on' state / DNA Damage Recognition in GG-NER / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / G1/S transition of mitotic cell cycle / negative regulation of canonical Wnt signaling pathway / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / protein modification process / modification-dependent protein catabolic process / RING-type E3 ubiquitin transferase / calcium channel activity / Degradation of beta-catenin by the destruction complex / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / protein localization / Inactivation of CSF3 (G-CSF) signaling / Dual Incision in GG-NER / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / NOTCH1 Intracellular Domain Regulates Transcription / protein tag activity / Formation of TC-NER Pre-Incision Complex / Downregulation of ERBB2 signaling / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / Formation of Incision Complex in GG-NER / Regulation of expression of SLITs and ROBOs / Interleukin-1 signaling / Dual incision in TC-NER / protein polyubiquitination / Orc1 removal from chromatin / Gap-filling DNA repair synthesis and ligation in TC-NER / Regulation of RAS by GAPs / ubiquitin-protein transferase activity / positive regulation of protein catabolic process / Regulation of RUNX2 expression and activity / UCH proteinases / cellular response to UV / ubiquitin protein ligase activity / KEAP1-NFE2L2 pathway / MAPK cascade / protein-macromolecule adaptor activity / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Antigen processing: Ubiquitination & Proteasome degradation / Cargo recognition for clathrin-mediated endocytosis / signaling receptor activity / Neddylation / ubiquitin-dependent protein catabolic process / spermatogenesis / proteasome-mediated ubiquitin-dependent protein catabolic process / positive regulation of canonical NF-kappaB signal transduction / RNA polymerase II-specific DNA-binding transcription factor binding / Potential therapeutics for SARS / molecular adaptor activity / protein ubiquitination / DNA repair / DNA damage response / ubiquitin protein ligase binding / regulation of transcription by RNA polymerase II / proteolysis
Similarity search - Function
Cullin; Chain C, Domain 2 / Cullin Repeats / 5 helical Cullin repeat like / Nedd8-like ubiquitin / Zinc finger, RING-H2-type / RING-H2 zinc finger domain / Cullin protein neddylation domain / Cullin, conserved site / Cullin family signature. / Cullin ...Cullin; Chain C, Domain 2 / Cullin Repeats / 5 helical Cullin repeat like / Nedd8-like ubiquitin / Zinc finger, RING-H2-type / RING-H2 zinc finger domain / Cullin protein neddylation domain / Cullin, conserved site / Cullin family signature. / Cullin / Cullin repeat-like-containing domain superfamily / Cullin protein, neddylation domain / Cullin protein neddylation domain / Cullin / Cullin, N-terminal / Cullin homology domain / Cullin homology domain superfamily / Cullin family / Cullin family profile. / Ribosomal Protein S5; domain 2 / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin conserved site / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Ubiquitin domain / Zinc finger RING-type profile. / Zinc finger, RING-type / Ubiquitin domain signature. / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin-like domain / Ubiquitin domain profile. / Arc Repressor Mutant, subunit A / Ubiquitin-like domain superfamily / Zinc finger, RING/FYVE/PHD-type / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Roll / Up-down Bundle / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
E3 ubiquitin-protein ligase RBX1 / NEDD8 / Cullin-5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3 Å
AuthorsDuda, D.M. / Borg, L.A. / Scott, D.C. / Hunt, H.W. / Hammel, M. / Schulman, B.A.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2008
Title: Structural insights into NEDD8 activation of cullin-RING ligases: conformational control of conjugation.
Authors: Duda, D.M. / Borg, L.A. / Scott, D.C. / Hunt, H.W. / Hammel, M. / Schulman, B.A.
History
DepositionJul 9, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: NEDD8
C: Cullin-5
R: Rbx1
B: NEDD8
D: Cullin-5
Y: Rbx1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,11912
Polymers133,7276
Non-polymers3926
Water0
1
A: NEDD8
C: Cullin-5
R: Rbx1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,0606
Polymers66,8633
Non-polymers1963
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: NEDD8
D: Cullin-5
Y: Rbx1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,0606
Polymers66,8633
Non-polymers1963
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: NEDD8
D: Cullin-5
Y: Rbx1
hetero molecules

A: NEDD8
C: Cullin-5
R: Rbx1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,11912
Polymers133,7276
Non-polymers3926
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_544-x,y-1/2,-z-1/21
Buried area17590 Å2
ΔGint-103 kcal/mol
Surface area52140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.315, 122.442, 128.647
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein NEDD8 / / Ubiquitin-like protein Nedd8 / Neddylin


Mass: 9078.012 Da / Num. of mol.: 2 / Fragment: NEDD8 C-terminus covalently linked to Cul5 Lys724 / Mutation: L162M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NEDD8 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15843
#2: Protein Cullin-5 / / CUL-5 / Vasopressin-activated calcium-mobilizing receptor / VACM-1


Mass: 45601.828 Da / Num. of mol.: 2 / Fragment: Cullin-5 residues 401-780 / Mutation: L407E, L439K, V440K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CUL5, VACM1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q93034
#3: Protein Rbx1 / / Rbx1 / Regulator of cullins 1 / RING finger protein 75 / Protein ZYP


Mass: 12183.467 Da / Num. of mol.: 2 / Fragment: Rbx1 residues 5-108
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RBX1, RNF75, ROC1 / Production host: Escherichia coli (E. coli) / References: UniProt: P62877
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 52.7 %
Crystal growTemperature: 277 K
Details: with ~19% PEG3350, 275mM (NH4)2PO4, 5mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 277K

-
Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 28564 / Biso Wilson estimate: 92.18 Å2 / Rsym value: 0.125
Reflection shellResolution: 3→3.11 Å / Redundancy: 6.1 % / Mean I/σ(I) obs: 2.4 / Rsym value: 0.678 / % possible all: 96.7

-
Processing

Software
NameVersionClassification
SOLVEphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 3→50 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1634466.22 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.299 1415 5 %RANDOM
Rwork0.249 ---
obs0.249 28357 99.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 19.636 Å2 / ksol: 0.273459 e/Å3
Displacement parametersBiso mean: 74.4 Å2
Baniso -1Baniso -2Baniso -3
1-23.09 Å20 Å20 Å2
2---21.75 Å20 Å2
3----1.35 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.43 Å
Luzzati d res low-5 Å
Luzzati sigma a0.64 Å0.6 Å
Refinement stepCycle: LAST / Resolution: 3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8833 0 6 0 8839
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.87
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 3→3.19 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.455 211 4.7 %
Rwork0.406 4270 -
obs--95.5 %

+
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