[English] 日本語
Yorodumi
- PDB-4fla: Crystal structure of human RPRD1B, carboxy-terminal domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4fla
TitleCrystal structure of human RPRD1B, carboxy-terminal domain
ComponentsRegulation of nuclear pre-mRNA domain-containing protein 1B
KeywordsTRANSCRIPTION / Structural Genomics Consortium / SGC
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
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2560 / : / 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. / ENTH/VHS / Single alpha-helices involved in coiled-coils or other helix-helix interfaces ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2560 / : / 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. / ENTH/VHS / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special
Similarity search - Domain/homology
Regulation of nuclear pre-mRNA domain-containing protein 1B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 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: Nat.Struct.Mol.Biol. / Year: 2014
Title: RPRD1A and RPRD1B are human RNA polymerase II C-terminal domain scaffolds for Ser5 dephosphorylation.
Authors: Ni, Z. / Xu, C. / Guo, X. / Hunter, G.O. / Kuznetsova, O.V. / Tempel, W. / Marcon, E. / Zhong, G. / Guo, H. / Kuo, W.H. / Li, J. / Young, P. / Olsen, J.B. / Wan, C. / Loppnau, P. / El ...Authors: Ni, Z. / Xu, C. / Guo, X. / Hunter, G.O. / Kuznetsova, O.V. / Tempel, W. / Marcon, E. / Zhong, G. / Guo, H. / Kuo, W.H. / Li, J. / Young, P. / Olsen, J.B. / Wan, C. / Loppnau, P. / El Bakkouri, M. / Senisterra, G.A. / He, H. / Huang, H. / Sidhu, S.S. / Emili, A. / Murphy, S. / Mosley, A.L. / Arrowsmith, C.H. / Min, J. / Greenblatt, J.F.
History
DepositionJun 14, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 22, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 16, 2014Group: Database references
Revision 1.2Aug 20, 2014Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
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
C: Regulation of nuclear pre-mRNA domain-containing protein 1B
D: Regulation of nuclear pre-mRNA domain-containing protein 1B


Theoretical massNumber of molelcules
Total (without water)69,46311
Polymers69,4634
Non-polymers07
Water2,666148
1
A: Regulation of nuclear pre-mRNA domain-containing protein 1B
B: Regulation of nuclear pre-mRNA domain-containing protein 1B


Theoretical massNumber of molelcules
Total (without water)34,7315
Polymers34,7312
Non-polymers03
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6010 Å2
ΔGint-53 kcal/mol
Surface area14670 Å2
MethodPISA
2
C: Regulation of nuclear pre-mRNA domain-containing protein 1B
D: Regulation of nuclear pre-mRNA domain-containing protein 1B


Theoretical massNumber of molelcules
Total (without water)34,7316
Polymers34,7312
Non-polymers04
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6080 Å2
ΔGint-50 kcal/mol
Surface area15140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.221, 100.221, 142.887
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number90
Space group name H-MP4212

-
Components

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


Mass: 17365.674 Da / Num. of mol.: 4 / Fragment: UNP residues 172-305
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RPRD1B, C20orf77, CREPT / Plasmid: pET28 MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9NQG5
#2: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 7 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 148 / 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: 3.1 Å3/Da / Density % sol: 60.3 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 7.5
Details: 25% PEG-3350, 0.2M ammonium acetate, 0.1M HEPES, pH 7.5, vapor diffusion, temperature 291K

-
Data collection

Diffraction
IDCrystal-ID
11
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 19-ID10.97931
SYNCHROTRONAPS 23-ID-B20.97944
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDFeb 24, 2012
MARMOSAIC 300 mm CCD2CCD
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.979311
20.979441
ReflectionResolution: 2.2→47.63 Å / Num. obs: 37701 / % possible obs: 99.98 % / Redundancy: 9.62 % / Rmerge(I) obs: 0.116 / Net I/σ(I): 15.5351
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allDiffraction-ID% possible all
2.2-2.329.810.935284653871,2100
2.32-2.469.80.655038251401,299.98
2.46-2.639.80.434724948191,2100
2.63-2.849.770.34400745031,299.98
2.84-3.119.740.184055341631,299.97
3.11-3.489.670.113671137981,2100
3.48-4.029.530.063212733721,2100
4.02-4.929.260.042668828811,2100
4.92-6.969.150.052092722871,299.95
6.96-47.638.410.021136113511,299.59

-
Processing

Software
NameVersionClassificationNB
SCALACCP4_3.3.20data scaling
SHELXphasing
RESOLVEphasing
REFMAC5.7.0027refinement
PDB_EXTRACT3.11data extraction
XDSdata reduction
RefinementMethod to determine structure: SAD / Resolution: 2.2→40 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.923 / WRfactor Rfree: 0.235 / WRfactor Rwork: 0.207 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 11.46 / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.236 / ESU R Free: 0.194 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED. unmerged intensities (SCALEPACK) for a selenomethionine derivative are included with the deposited structure ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED. unmerged intensities (SCALEPACK) for a selenomethionine derivative are included with the deposited structure factors. Discontinuities and ambiguity of electron density defining residues 190 through 194 cause us to question the register of the amino acid sequence fitted N-terminal of that region. The programs resolve, arp/warp, dm were used in density improvement of the original Se-Met maps. Buccaneer was used for model tracing. COOT and the MOLPROBITY server were also used during refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.2575 1587 4.212 %thin shells (sftools)
Rwork0.2316 ---
obs0.233 37678 99.867 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso max: 94.95 Å2 / Biso mean: 44.226 Å2 / Biso min: 13.84 Å2
Baniso -1Baniso -2Baniso -3
1-1.791 Å20 Å20 Å2
2--1.791 Å20 Å2
3----3.583 Å2
Refinement stepCycle: LAST / Resolution: 2.2→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3871 0 7 148 4026
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0193970
X-RAY DIFFRACTIONr_bond_other_d0.0070.023966
X-RAY DIFFRACTIONr_angle_refined_deg1.3112.0025360
X-RAY DIFFRACTIONr_angle_other_deg1.32639118
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.1735511
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.54425.48177
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.35115802
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.1811532
X-RAY DIFFRACTIONr_chiral_restr0.0660.2663
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024425
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02775
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2-2.2570.3641200.29126012721100
2.257-2.3190.3231120.2825412653100
2.319-2.3860.2921040.2492500260599.962
2.386-2.4590.2621000.24224232523100
2.459-2.5390.2451000.25123242424100
2.539-2.62800.26123722372100
2.628-2.7270.2651540.24821392293100
2.727-2.8370.2891480.2422063221299.955
2.837-2.96300.2482121212299.953
2.963-3.1070.2881300.25518962026100
3.107-3.2740.31080.24318181926100
3.274-3.4710.2541020.24417601862100
3.471-3.70800.21717411741100
3.708-4.0030.217930.19815331626100
4.003-4.380.215720.17914381510100
4.38-4.890.202600.16713161376100
4.89-5.6320.249800.2461152123399.919
5.632-6.8640.225360.27610171053100
6.864-9.5680.311330.192824857100
9.568-400.23350.27850754998.725
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)
10.0023-0.0353-0.09881.18643.452210.0747-0.0069-0.00490.0046-0.1073-0.13290.0569-0.3614-0.44440.13970.42590.01230.00510.1418-0.00830.1827.076147.8861.546
20.3306-0.5695-1.85271.00983.200510.3981-0.14250.0565-0.05040.1408-0.10.09870.7552-0.29480.24250.42660.0041-0.00280.1531-0.04220.174526.036751.55673.6678
30.0311-0.1087-0.37250.95242.88038.906-0.0560.03480.00090.0752-0.07490.08970.2728-0.29410.13090.1787-0.01990.02030.086-0.00080.168128.090154.29389.4048
40.19450.46481.43151.14343.439710.5701-0.0663-0.03650.027-0.073-0.09590.0931-0.414-0.27960.16220.23010.02390.02680.0848-0.02670.151427.688951.0781-2.5833
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A176 - 301
2X-RAY DIFFRACTION2B176 - 301
3X-RAY DIFFRACTION3C175 - 301
4X-RAY DIFFRACTION4D175 - 301

+
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