[English] 日本語
Yorodumi
- PDB-4fu3: CID of human RPRD1B -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4fu3
TitleCID of human RPRD1B
ComponentsRegulation of nuclear pre-mRNA domain-containing protein 1B
KeywordsTRANSCRIPTION / Structural Genomics Consortium / SGC / domain swapping
Function / homology
Function and homology information


regulation of cell cycle process / RNA polymerase II promoter clearance / mRNA 3'-end processing / transcription preinitiation complex / RNA polymerase II complex binding / RNA polymerase II C-terminal domain binding / RNA polymerase II transcribes snRNA genes / positive regulation of cell population proliferation / positive regulation of transcription by RNA polymerase II / nucleoplasm ...regulation of cell cycle process / RNA polymerase II promoter clearance / mRNA 3'-end processing / transcription preinitiation complex / RNA polymerase II complex binding / RNA polymerase II C-terminal domain binding / RNA polymerase II transcribes snRNA genes / positive regulation of cell population proliferation / positive regulation of transcription by RNA polymerase II / nucleoplasm / identical protein binding / nucleus
Similarity search - Function
: / Regulation of nuclear pre-mRNA domain-containing protein 1A/B / Cell-cycle alteration and expression-elevated protein in tumour / CID domain / RPR / CID domain / CID domain profile. / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #90 / ENTH/VHS / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat ...: / Regulation of nuclear pre-mRNA domain-containing protein 1A/B / Cell-cycle alteration and expression-elevated protein in tumour / CID domain / RPR / CID domain / CID domain profile. / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #90 / ENTH/VHS / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha
Similarity search - Domain/homology
Regulation of nuclear pre-mRNA domain-containing protein 1B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsNi, Z. / Xu, C. / Tempel, W. / El Bakkouri, M. / Loppnau, P. / Guo, X. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. ...Ni, Z. / Xu, C. / Tempel, W. / El Bakkouri, M. / Loppnau, P. / Guo, X. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. / Greenblatt, J.F. / Structural Genomics Consortium (SGC)
CitationJournal: TO BE PUBLISHED
Title: CID of human RPRD1B
Authors: Ni, Z. / Xu, C. / Tempel, W. / El Bakkouri, M. / Loppnau, P. / Guo, X. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. / Greenblatt, J.F.
History
DepositionJun 28, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 29, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2024Group: 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_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: Regulation of nuclear pre-mRNA domain-containing protein 1B
B: Regulation of nuclear pre-mRNA domain-containing protein 1B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,30115
Polymers31,1952
Non-polymers10613
Water1,36976
1
A: Regulation of nuclear pre-mRNA domain-containing protein 1B
B: Regulation of nuclear pre-mRNA domain-containing protein 1B
hetero molecules

A: Regulation of nuclear pre-mRNA domain-containing protein 1B
B: Regulation of nuclear pre-mRNA domain-containing protein 1B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,60330
Polymers62,3904
Non-polymers21326
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area10600 Å2
ΔGint-71 kcal/mol
Surface area22700 Å2
MethodPISA
2
A: Regulation of nuclear pre-mRNA domain-containing protein 1B
hetero molecules

A: Regulation of nuclear pre-mRNA domain-containing protein 1B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,33718
Polymers31,1952
Non-polymers14216
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area2970 Å2
ΔGint-34 kcal/mol
Surface area13580 Å2
MethodPISA
3
B: Regulation of nuclear pre-mRNA domain-containing protein 1B
hetero molecules

B: Regulation of nuclear pre-mRNA domain-containing protein 1B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,26612
Polymers31,1952
Non-polymers7110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area3070 Å2
ΔGint-34 kcal/mol
Surface area13680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.752, 79.784, 108.666
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein Regulation of nuclear pre-mRNA domain-containing protein 1B / Cell cycle-related and expression-elevated protein in tumor


Mass: 15597.543 Da / Num. of mol.: 2 / Fragment: UNP residues 2-235
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RPRD1B, C20orf77, CREPT / Plasmid: pET15 MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9NQG5
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 10 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 76 / 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: 41.7 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 8.5
Details: 30% PEG-4000, 0.2M magnesium chloride, 0.1M TRIS hydrochloride, pH 8.5, vapor diffusion, temperature 291K

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
chess1001
11
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9179 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 19, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9179 Å / Relative weight: 1
ReflectionResolution: 1.9→46.78 Å / Num. obs: 20170 / % possible obs: 99.95 % / Redundancy: 7.19 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 19.6638
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allDiffraction-ID% possible all
1.9-27.110.98204382875199.96
2-2.127.20.53200502785199.98
2.12-2.277.290.31187362570199.98
2.27-2.457.330.191778224271100
2.45-2.697.330.121629522231100
2.69-37.320.071488120321100
3-3.477.280.041308917971100
3.47-4.257.180.031107915441100
4.25-6.016.930.03843212171100
6.01-46.785.950.034163700198.82

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
SCALACCP4_3.3.20data scaling
MOLREPphasing
BUSTER-TNTBUSTER 2.10.0refinement
PDB_EXTRACT3.11data extraction
XDSdata reduction
BUSTER2.10.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: unpublished model of same protein, different crystal form

Resolution: 1.9→19.77 Å / Cor.coef. Fo:Fc: 0.9456 / Cor.coef. Fo:Fc free: 0.8974 / Occupancy max: 1 / Occupancy min: 0.5 / SU R Cruickshank DPI: 0.17 / Cross valid method: THROUGHOUT / σ(F): 0
Details: DM, PARROT, ARP/WARP, REFMAC, COOT and the MOLPROBITY server were also used.
RfactorNum. reflection% reflectionSelection details
Rfree0.2589 1048 5.21 %THIN SHELLS (SFTOOLS)
Rwork0.209 ---
obs0.2116 20125 99.94 %-
Displacement parametersBiso max: 107.05 Å2 / Biso mean: 37.5815 Å2 / Biso min: 16.61 Å2
Baniso -1Baniso -2Baniso -3
1-0.4705 Å20 Å20 Å2
2---1.5618 Å20 Å2
3---1.0913 Å2
Refine analyzeLuzzati coordinate error obs: 0.301 Å
Refinement stepCycle: LAST / Resolution: 1.9→19.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2012 0 13 76 2101
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d752SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes50HARMONIC2
X-RAY DIFFRACTIONt_gen_planes314HARMONIC5
X-RAY DIFFRACTIONt_it2098HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion267SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2509SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2098HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg2840HARMONIC21
X-RAY DIFFRACTIONt_omega_torsion2.63
X-RAY DIFFRACTIONt_other_torsion18.36
LS refinement shellResolution: 1.9→2 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.2287 129 4.49 %
Rwork0.2205 2743 -
all0.2209 2872 -
obs--99.94 %
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)
10.42230.1830.00730.3120.14921.1042-0.00140.00630.07880.0249-0.10190.1063-0.0927-0.1440.1033-0.05660.06150.0232-0.11710.01270.1246-6.332717.668117.2787
21.35560.5717-0.6850.2002-0.37052.35310.00090.0718-0.09550.0855-0.03990.04430.13220.32730.039-0.030.086-0.0321-0.05490.0002-0.032111.14342.651723.2685
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A2 - 129
2X-RAY DIFFRACTION2{ B|* }B2 - 129

+
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