[English] 日本語
Yorodumi
- PDB-3tdu: N-terminal acetylation acts as an avidity enhancer within an inte... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3tdu
TitleN-terminal acetylation acts as an avidity enhancer within an interconnected multiprotein complex: Structure of a human Cul1WHB-Dcn1P-acetylated Ubc12N complex
Components
  • Cullin-1
  • DCN1-like protein 1
  • NEDD8-conjugating enzyme Ubc12
KeywordsLigase/protein binding / E2:E3 / Ligase-protein binding complex
Function / homology
Function and homology information


E2 NEDD8-conjugating enzyme / NEDD8 conjugating enzyme activity / positive regulation of protein neddylation / ubiquitin-like protein binding / Parkin-FBXW7-Cul1 ubiquitin ligase complex / regulation of protein neddylation / NEDD8 transferase activity / cullin-RING ubiquitin ligase complex / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / protein neddylation ...E2 NEDD8-conjugating enzyme / NEDD8 conjugating enzyme activity / positive regulation of protein neddylation / ubiquitin-like protein binding / Parkin-FBXW7-Cul1 ubiquitin ligase complex / regulation of protein neddylation / NEDD8 transferase activity / cullin-RING ubiquitin ligase complex / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / protein neddylation / ubiquitin conjugating enzyme binding / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / SCF ubiquitin ligase complex / ubiquitin ligase complex scaffold activity / Prolactin receptor signaling / protein monoubiquitination / TGF-beta receptor signaling activates SMADs / cullin family protein binding / regulation of protein ubiquitination / protein K48-linked ubiquitination / Nuclear events stimulated by ALK signaling in cancer / ubiquitin ligase complex / Regulation of BACH1 activity / post-translational protein modification / MAP3K8 (TPL2)-dependent MAPK1/3 activation / intrinsic apoptotic signaling pathway / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / Dectin-1 mediated noncanonical NF-kB signaling / Degradation of GLI1 by the proteasome / Activation of NF-kappaB in B cells / Negative regulation of NOTCH4 signaling / animal organ morphogenesis / Iron uptake and transport / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / G1/S transition of mitotic cell cycle / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / protein modification process / Degradation of beta-catenin by the destruction complex / NOTCH1 Intracellular Domain Regulates Transcription / CLEC7A (Dectin-1) signaling / SCF(Skp2)-mediated degradation of p27/p21 / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / FCERI mediated NF-kB activation / Interleukin-1 signaling / Orc1 removal from chromatin / ubiquitin-protein transferase activity / positive regulation of neuron apoptotic process / Regulation of RUNX2 expression and activity / Cyclin D associated events in G1 / Regulation of PLK1 Activity at G2/M Transition / protein-macromolecule adaptor activity / Antigen processing: Ubiquitination & Proteasome degradation / Circadian Clock / Downstream TCR signaling / Neddylation / proteasome-mediated ubiquitin-dependent protein catabolic process / positive regulation of canonical NF-kappaB signal transduction / cell population proliferation / protein ubiquitination / ubiquitin protein ligase binding / nucleoplasm / ATP binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Potentiating neddylation domain / Defective-in-cullin neddylation protein / DCN1-like, PONY binding domain / Cullin binding / DCUN1 domain profile. / UBA-like domain / Cullin protein neddylation domain / Cullin, conserved site / Cullin family signature. / Cullin ...Potentiating neddylation domain / Defective-in-cullin neddylation protein / DCN1-like, PONY binding domain / Cullin binding / DCUN1 domain profile. / UBA-like 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. / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / UBA-like superfamily / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme/RWD-like / EF-hand / Recoverin; domain 1 / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
NEDD8-conjugating enzyme Ubc12 / Cullin-1 / DCN1-like protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
HOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsScott, D.C. / Monda, J.K. / Bennett, E.J. / Harper, J.W. / Schulman, B.A.
CitationJournal: Science / Year: 2011
Title: N-terminal acetylation acts as an avidity enhancer within an interconnected multiprotein complex.
Authors: Scott, D.C. / Monda, J.K. / Bennett, E.J. / Harper, J.W. / Schulman, B.A.
History
DepositionAug 11, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 23, 2011Group: Database references
Revision 1.2Nov 8, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
Revision 1.3Apr 18, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.4Jan 29, 2020Group: Advisory / Database references / Derived calculations
Category: pdbx_distant_solvent_atoms / pdbx_struct_assembly ...pdbx_distant_solvent_atoms / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / struct_conn / struct_ref_seq_dif
Item: _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details ..._pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.5Sep 13, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.6Mar 13, 2024Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Item: _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details ..._pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DCN1-like protein 1
B: DCN1-like protein 1
C: Cullin-1
D: Cullin-1
E: NEDD8-conjugating enzyme Ubc12
F: NEDD8-conjugating enzyme Ubc12


Theoretical massNumber of molelcules
Total (without water)68,3256
Polymers68,3256
Non-polymers00
Water10,611589
1
A: DCN1-like protein 1
C: Cullin-1
F: NEDD8-conjugating enzyme Ubc12


Theoretical massNumber of molelcules
Total (without water)34,1623
Polymers34,1623
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DCN1-like protein 1
D: Cullin-1
E: NEDD8-conjugating enzyme Ubc12


Theoretical massNumber of molelcules
Total (without water)34,1623
Polymers34,1623
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)135.431, 65.454, 64.182
Angle α, β, γ (deg.)90.00, 104.73, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11D-145-

HOH

-
Components

#1: Protein DCN1-like protein 1 / DCUN1 domain-containing protein 1 / Defective in cullin neddylation protein 1-like protein 1 / ...DCUN1 domain-containing protein 1 / Defective in cullin neddylation protein 1-like protein 1 / Squamous cell carcinoma-related oncogene


Mass: 23237.461 Da / Num. of mol.: 2 / Fragment: unp residues 62-259
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DCUN1D1, DCUN1L1, RP42, SCCRO / Plasmid: pGEX / Production host: Escherichia coli (E. coli) / References: UniProt: Q96GG9
#2: Protein Cullin-1 / / CUL-1


Mass: 9015.699 Da / Num. of mol.: 2 / Fragment: unp residues 702-776
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CUL1 / Plasmid: pGEX / Production host: Escherichia coli (E. coli) / References: UniProt: Q13616
#3: Protein/peptide NEDD8-conjugating enzyme Ubc12 / NEDD8 carrier protein / NEDD8 protein ligase / Ubiquitin-conjugating enzyme E2 M


Mass: 1909.292 Da / Num. of mol.: 2 / Fragment: unp residues 2-15 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human)
References: UniProt: P61081, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 589 / 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: 2.01 Å3/Da / Density % sol: 38.88 %
Crystal growTemperature: 276 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 27% PEG1500, 0.1M MIB, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 276K

-
Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 9, 2010
RadiationMonochromator: Double Crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. all: 86181 / Num. obs: 78739 / % possible obs: 96.2 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 2.605 / Redundancy: 3.7 % / Rmerge(I) obs: 0.09 / Rsym value: 0.09
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRsym valueDiffraction-ID% possible all
1.5-1.553.30.4132.60.413188
1.55-1.62195.4
1.69-1.92195.6
1.69-1.78196.1
1.78-1.89196.6
1.89-2.04197.1

-
Processing

Software
NameVersionClassification
BSSdata collection
CCP4model building
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1LDJ

1ldj


Resolution: 1.5→50 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.939 / SU B: 3.716 / SU ML: 0.063 / Cross valid method: THROUGHOUT / ESU R Free: 0.094 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23249 4150 5 %RANDOM
Rwork0.20606 ---
obs0.20738 78739 96.08 %-
all-86181 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.829 Å2
Baniso -1Baniso -2Baniso -3
1-1.55 Å2-0 Å20.39 Å2
2---1.48 Å2-0 Å2
3---0.14 Å2
Refinement stepCycle: LAST / Resolution: 1.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4690 0 0 589 5279
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0224880
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9151.9796561
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.2135589
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.22324.793242
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.34915975
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4661530
X-RAY DIFFRACTIONr_chiral_restr0.0710.2702
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213642
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.621.52877
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.39924648
X-RAY DIFFRACTIONr_scbond_it4.67432003
X-RAY DIFFRACTIONr_scangle_it8.1374.51897
X-RAY DIFFRACTIONr_rigid_bond_restr2.45834880
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.503→1.542 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.356 261 -
Rwork0.326 5070 -
obs--84.32 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.0639-0.00950.00440.0211-0.01570.00450.00790.0037-0.006-0.0128-0.00640.00160.00570.0036-0.00150.0256-0.0013-0.00650.02870.00090.031723.1649-4.3659-26.5951
20.0387-0.017-0.02270.0063-0.01480.06750.00010.0067-0.00260.0092-0.00030.0065-0.0283-0.01050.00020.0191-0.0024-0.0110.02990.00250.035714.888-7.10514.4874
30.11850.27730.10611.36210.22440.04560.0047-0.02030.0087-0.0208-0.0105-0.03450.0051-0.00770.00580.0056-0.0021-0.00360.03660.0070.017823.475926.0957-27.8761
40.0216-0.20950.16361.0133-0.5890.41320.02270.0054-0.00180.019-0.02870.04090.02670.02680.00610.02160.00190.00060.03060.00030.026213.9925-37.73524.9822
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A60 - 252
2X-RAY DIFFRACTION1A60 - 252
3X-RAY DIFFRACTION2B60 - 253
4X-RAY DIFFRACTION2B60 - 253
5X-RAY DIFFRACTION3C702 - 776
6X-RAY DIFFRACTION3C24 - 547
7X-RAY DIFFRACTION4D701 - 776
8X-RAY DIFFRACTION4D48 - 597

+
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