[English] 日本語
Yorodumi
- PDB-2fv2: Crystal Structure Analysis of human Rcd-1 conserved region -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2fv2
TitleCrystal Structure Analysis of human Rcd-1 conserved region
ComponentsRCD1 required for cell differentiation1 homolog
KeywordsTRANSCRIPTION / ARMADILLO-REPEAT
Function / homology
Function and homology information


CCR4-NOT core complex / CCR4-NOT complex / negative regulation of intracellular estrogen receptor signaling pathway / nuclear-transcribed mRNA poly(A) tail shortening / sex differentiation / Deadenylation of mRNA / M-decay: degradation of maternal mRNAs by maternally stored factors / regulatory ncRNA-mediated gene silencing / TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain / positive regulation of epidermal growth factor receptor signaling pathway ...CCR4-NOT core complex / CCR4-NOT complex / negative regulation of intracellular estrogen receptor signaling pathway / nuclear-transcribed mRNA poly(A) tail shortening / sex differentiation / Deadenylation of mRNA / M-decay: degradation of maternal mRNAs by maternally stored factors / regulatory ncRNA-mediated gene silencing / TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain / positive regulation of epidermal growth factor receptor signaling pathway / epidermal growth factor receptor binding / nuclear receptor coactivator activity / P-body / kinase binding / Activation of anterior HOX genes in hindbrain development during early embryogenesis / cytokine-mediated signaling pathway / positive regulation of peptidyl-serine phosphorylation / negative regulation of translation / protein domain specific binding / protein homodimerization activity / protein-containing complex / membrane / nucleus / cytosol
Similarity search - Function
CCR4-NOT transcription complex subunit 9 / Cell differentiation family, Rcd1-like / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
: / : / CCR4-NOT transcription complex subunit 9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsGarces, R.G. / Gillon, W. / Pai, E.F.
CitationJournal: Protein Sci. / Year: 2007
Title: Atomic model of human Rcd-1 reveals an armadillo-like-repeat protein with in vitro nucleic acid binding properties.
Authors: Garces, R.G. / Gillon, W. / Pai, E.F.
History
DepositionJan 28, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 9, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: RCD1 required for cell differentiation1 homolog
B: RCD1 required for cell differentiation1 homolog
C: RCD1 required for cell differentiation1 homolog
D: RCD1 required for cell differentiation1 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,1415
Polymers122,0864
Non-polymers551
Water11,908661
1
A: RCD1 required for cell differentiation1 homolog
B: RCD1 required for cell differentiation1 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,0983
Polymers61,0432
Non-polymers551
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1910 Å2
ΔGint-17 kcal/mol
Surface area24060 Å2
MethodPISA
2
C: RCD1 required for cell differentiation1 homolog
D: RCD1 required for cell differentiation1 homolog


Theoretical massNumber of molelcules
Total (without water)61,0432
Polymers61,0432
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2010 Å2
ΔGint-16 kcal/mol
Surface area24020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.508, 68.963, 69.361
Angle α, β, γ (deg.)94.16, 117.26, 91.91
Int Tables number1
Space group name H-MP1
DetailsBiological assembly appears to be a homodimer. 2 dimers are found per asymmetric unit.

-
Components

#1: Protein
RCD1 required for cell differentiation1 homolog


Mass: 30521.500 Da / Num. of mol.: 4 / Fragment: (Residues: 18 - 285)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: Rcd1 / Plasmid: pET 32 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Codon Plus / References: GenBank: 4885579, UniProt: Q92600*PLUS
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 661 / 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: 2.37 Å3/Da / Density % sol: 48.14 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.7
Details: 100 mM MES pH5.7, 115 mM MnSO4, 17% PEG 3350, 1% glucose, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

-
Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-D / Wavelength: 0.9568, 0.9795, 0.9797, 0.9407
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 5, 2005
RadiationMonochromator: Si (111) double-crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.95681
20.97951
30.97971
40.94071
ReflectionResolution: 2.2→50 Å / Num. all: 152086 / Num. obs: 53307 / % possible obs: 95.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 13.3 Å2 / Rmerge(I) obs: 0.036 / Rsym value: 0.033
Reflection shellResolution: 2.2→2.28 Å / % possible all: 89.7

-
Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
SnBphasing
RefinementMethod to determine structure: MAD / Resolution: 2.2→27.26 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 550645.53 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.279 4247 8.2 %RANDOM
Rwork0.217 ---
all0.279 152086 --
obs0.217 51688 91 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 48.2372 Å2 / ksol: 0.346933 e/Å3
Displacement parametersBiso mean: 29.6 Å2
Baniso -1Baniso -2Baniso -3
1--1.84 Å22.64 Å23.44 Å2
2---2.67 Å23.38 Å2
3---4.51 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.31 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 2.2→27.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8549 0 1 661 9211
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d18.8
X-RAY DIFFRACTIONc_improper_angle_d0.88
X-RAY DIFFRACTIONc_mcbond_it1.121.5
X-RAY DIFFRACTIONc_mcangle_it1.82
X-RAY DIFFRACTIONc_scbond_it1.692
X-RAY DIFFRACTIONc_scangle_it2.462.5
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.327 552 8.1 %
Rwork0.244 6288 -
obs--72.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3ion.param

+
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