[English] 日本語
Yorodumi
- PDB-2ogb: Crystal structure of the C-terminal domain of mouse Nrdp1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2ogb
TitleCrystal structure of the C-terminal domain of mouse Nrdp1
ComponentsRING finger protein 41
KeywordsLIGASE / E3 ubiquitin ligase / Receptor-binding region
Function / homology
Function and homology information


regulation of lymphocyte differentiation / small GTPase binding => GO:0031267 / interleukin-3 receptor binding / erythropoietin receptor binding / regulation of myeloid cell differentiation / Downregulation of ERBB2:ERBB3 signaling / endoplasmic reticulum tubular network / Antigen processing: Ubiquitination & Proteasome degradation / regulation of establishment of cell polarity / negative regulation of mitophagy ...regulation of lymphocyte differentiation / small GTPase binding => GO:0031267 / interleukin-3 receptor binding / erythropoietin receptor binding / regulation of myeloid cell differentiation / Downregulation of ERBB2:ERBB3 signaling / endoplasmic reticulum tubular network / Antigen processing: Ubiquitination & Proteasome degradation / regulation of establishment of cell polarity / negative regulation of mitophagy / regulation of reactive oxygen species metabolic process / regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / regulation of MAPK cascade / protein autoubiquitination / extrinsic apoptotic signaling pathway / negative regulation of cell migration / proteasomal protein catabolic process / RING-type E3 ubiquitin transferase / receptor tyrosine kinase binding / autophagy / protein polyubiquitination / ubiquitin-protein transferase activity / positive regulation of protein catabolic process / positive regulation of reactive oxygen species metabolic process / ubiquitin protein ligase activity / positive regulation of DNA-binding transcription factor activity / regulation of gene expression / protein ubiquitination / protein domain specific binding / negative regulation of cell population proliferation / perinuclear region of cytoplasm / zinc ion binding / identical protein binding
Similarity search - Function
E3 ubiquitin-protein ligase NRDP1 / NRDP1, C-terminal / USP8 interacting / Zinc finger, SIAH-type / Zinc finger SIAH-type profile. / TRAF-like / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / Zinc finger RING-type profile. ...E3 ubiquitin-protein ligase NRDP1 / NRDP1, C-terminal / USP8 interacting / Zinc finger, SIAH-type / Zinc finger SIAH-type profile. / TRAF-like / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
THIOCYANATE ION / E3 ubiquitin-protein ligase NRDP1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.95 Å
AuthorsBouyain, S. / Leahy, D.J.
CitationJournal: Protein Sci. / Year: 2007
Title: Structure-based mutagenesis of the substrate-recognition domain of Nrdp1/FLRF identifies the binding site for the receptor tyrosine kinase ErbB3.
Authors: Bouyain, S. / Leahy, D.J.
History
DepositionJan 5, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 16, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / 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_conn.pdbx_leaving_atom_flag / _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: RING finger protein 41
B: RING finger protein 41
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2575
Polymers29,0152
Non-polymers2423
Water2,198122
1
A: RING finger protein 41
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,7504
Polymers14,5081
Non-polymers2423
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: RING finger protein 41


Theoretical massNumber of molelcules
Total (without water)14,5081
Polymers14,5081
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: RING finger protein 41

B: RING finger protein 41


Theoretical massNumber of molelcules
Total (without water)29,0152
Polymers29,0152
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area1390 Å2
ΔGint-10 kcal/mol
Surface area12830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)157.427, 58.227, 37.387
Angle α, β, γ (deg.)90.00, 101.53, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein RING finger protein 41 /


Mass: 14507.568 Da / Num. of mol.: 2 / Fragment: Nrdp1 C-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Rnf41 / Plasmid: pET41 / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q8BH75, ubiquitin-protein ligase
#2: Chemical ChemComp-SCN / THIOCYANATE ION / Thiocyanate


Mass: 58.082 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CNS
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 122 / 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: 2.89 Å3/Da / Density % sol: 57.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.4
Details: 25% (w/v) polyethylene glycol 8000, 180 mM potassium thiocyanate, 100 mM Tris-HCl, pH 8.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9792
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 27, 2005
RadiationMonochromator: KOHZU double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionRedundancy: 4.5 % / Av σ(I) over netI: 26.1 / Number: 89260 / Rmerge(I) obs: 0.092 / Χ2: 1.01 / D res high: 2 Å / D res low: 30 Å / Num. obs: 19750 / % possible obs: 86.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.313085.510.0780.9615.3
3.424.3189.510.0740.8835.3
2.993.4291.910.0920.9485.2
2.712.9992.210.1170.9375.2
2.522.7192.310.1431.0085.1
2.372.5293.110.1581.0794.9
2.252.3792.710.1831.1554.2
2.152.259110.2271.1393.7
2.072.1579.710.2751.1362.9
22.0760.910.3061.0942.4
ReflectionResolution: 1.95→30 Å / Num. obs: 20628 / % possible obs: 85.2 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.092 / Χ2: 0.993 / Net I/σ(I): 25.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.95-2.022.30.33613480.983156.6
2.02-2.12.70.28617500.958171.9
2.1-2.23.20.25220920.987187.1
2.2-2.313.90.19322110.995192.1
2.31-2.464.60.16222360.977192.8
2.46-2.654.90.14722480.984192.9
2.65-2.9150.1222250.974191.8
2.91-3.335.10.09522061.006191.6
3.33-4.25.10.07521931.001189.6
4.2-305.20.07721191.026185.1

-
Phasing

PhasingMethod: SAD
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Se26.5320.2550.4980.1660.92
2Se25.3190.7280.1460.2210.938
3Se41.5820.4330.1490.3780.906
4Se44.520.4460.0560.4690.992
5Se25.730.2680.4490.2280.683
6Se46.6780.3720.1550.4450.924
7Se35.9320.2460.1120.1120.797
8Se30.060.7630.1120.3270.646
9Se54.1880.4130.1820.141.09
10Se53.6510.610.1270.4781.121
11Se43.1390.5660.1290.1850.874
12Se46.2760.2160.0310.390.711
Phasing dmFOM : 0.6 / FOM acentric: 0.6 / FOM centric: 0.5 / Reflection: 15198 / Reflection acentric: 14480 / Reflection centric: 718
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
6.3-29.680.860.890.6761553481
3.9-6.30.870.890.7320151872143
3.1-3.90.80.810.625532425128
2.8-3.10.640.650.4426342515119
2.4-2.80.480.480.3346064447159
2.2-2.40.320.320.222775268788

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVE2.03phasing
RESOLVE2.03phasing
REFMACrefinement
PDB_EXTRACT2data extraction
ADSCQUANTUMdata collection
RefinementMethod to determine structure: SAD / Resolution: 1.95→20 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.932 / SU B: 9.879 / SU ML: 0.142 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.188 / ESU R Free: 0.155 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.234 972 4.8 %RANDOM
Rwork0.212 ---
obs0.213 20090 97.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 43.318 Å2
Baniso -1Baniso -2Baniso -3
1-1.68 Å20 Å20.8 Å2
2--0.46 Å20 Å2
3----1.82 Å2
Refinement stepCycle: LAST / Resolution: 1.95→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1960 0 15 122 2097
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222010
X-RAY DIFFRACTIONr_angle_refined_deg1.3731.952722
X-RAY DIFFRACTIONr_dihedral_angle_1_deg1.4635245
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.26324.4998
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.97915346
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5931516
X-RAY DIFFRACTIONr_chiral_restr0.0920.2299
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021530
X-RAY DIFFRACTIONr_nbd_refined0.2810.2974
X-RAY DIFFRACTIONr_nbtor_refined0.3250.21428
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.2128
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3820.286
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2260.217
X-RAY DIFFRACTIONr_mcbond_it1.5391.51237
X-RAY DIFFRACTIONr_mcangle_it2.86521999
X-RAY DIFFRACTIONr_scbond_it5.3343773
X-RAY DIFFRACTIONr_scangle_it8.7974.5723
LS refinement shellResolution: 1.95→2.002 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 43 -
Rwork0.307 801 -
obs-844 89.12 %
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)
11.8674-2.0104-1.43294.22532.49973.1592-0.0641-0.18690.06220.08860.0978-0.0424-0.01520.054-0.0338-0.25090.0061-0.0143-0.27960.0009-0.1915-38.629-0.4461.433
23.4371-0.3525-0.70832.4146-0.46624.90360.00160.0488-0.0899-0.1765-0.0038-0.21330.29580.89590.0022-0.22110.0497-0.037-0.0405-0.016-0.187-14.677-21.733-13.227
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA198 - 2967 - 105
21AA306 - 314115 - 123
32BB198 - 2967 - 105
42BB306 - 314115 - 123

+
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