[English] 日本語
Yorodumi
- PDB-3b4m: Crystal Structure of Human PABPN1 RRM -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3b4m
TitleCrystal Structure of Human PABPN1 RRM
ComponentsPolyadenylate-binding protein 2
KeywordsRNA BINDING PROTEIN / RRM fold / ALPHA-BETA Sandwich structure / RNA Binding Domain / RNA Recognition Motif / Acetylation / Alternative splicing / Coiled coil / Cytoplasm / Disease mutation / Methylation / mRNA processing / Nucleus / Polymorphism / RNA-binding / Triplet repeat expansion
Function / homology
Function and homology information


positive regulation of polynucleotide adenylyltransferase activity / Inhibition of Host mRNA Processing and RNA Silencing / Processing of Intronless Pre-mRNAs / Z-decay: degradation of maternal mRNAs by zygotically expressed factors / nuclear inclusion body / poly(A) binding / mRNA 3'-end processing / RNA polymerase binding / RNA Polymerase II Transcription Termination / poly(A)+ mRNA export from nucleus ...positive regulation of polynucleotide adenylyltransferase activity / Inhibition of Host mRNA Processing and RNA Silencing / Processing of Intronless Pre-mRNAs / Z-decay: degradation of maternal mRNAs by zygotically expressed factors / nuclear inclusion body / poly(A) binding / mRNA 3'-end processing / RNA polymerase binding / RNA Polymerase II Transcription Termination / poly(A)+ mRNA export from nucleus / Processing of Capped Intron-Containing Pre-mRNA / RNA processing / muscle contraction / mRNA processing / MAPK cascade / cellular response to lipopolysaccharide / nuclear speck / ribonucleoprotein complex / RNA binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
RRM (RNA recognition motif) domain / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Polyadenylate-binding protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.82 Å
AuthorsGe, H. / Zhou, D. / Teng, M. / Niu, L.
CitationJournal: Proteins / Year: 2008
Title: Crystal structure and possible dimerization of the single RRM of human PABPN1
Authors: Ge, H. / Zhou, D. / Tong, S. / Gao, Y. / Teng, M. / Niu, L.
History
DepositionOct 24, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: 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 / 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: Polyadenylate-binding protein 2
B: Polyadenylate-binding protein 2
C: Polyadenylate-binding protein 2
D: Polyadenylate-binding protein 2


Theoretical massNumber of molelcules
Total (without water)43,4454
Polymers43,4454
Non-polymers00
Water59433
1
A: Polyadenylate-binding protein 2
B: Polyadenylate-binding protein 2


Theoretical massNumber of molelcules
Total (without water)21,7222
Polymers21,7222
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1590 Å2
ΔGint-7.6 kcal/mol
Surface area8090 Å2
MethodPISA
2
C: Polyadenylate-binding protein 2
D: Polyadenylate-binding protein 2


Theoretical massNumber of molelcules
Total (without water)21,7222
Polymers21,7222
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1590 Å2
ΔGint-7.8 kcal/mol
Surface area8080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.338, 59.338, 80.599
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

-
Components

#1: Protein
Polyadenylate-binding protein 2 / Poly(A)-binding protein 2 / Poly(A)-binding protein II / PABII / Polyadenylate-binding nuclear ...Poly(A)-binding protein 2 / Poly(A)-binding protein II / PABII / Polyadenylate-binding nuclear protein 1 / Nuclear poly(A)-binding protein 1


Mass: 10861.189 Da / Num. of mol.: 4 / Fragment: UNP residues 167-254
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PABPN1, PAB2, PABP2 / Plasmid: pET22b(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q86U42
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 1.89 Å3/Da / Density % sol: 34.77 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES, 4.2M sodium chloride, pH7.5, VAPOR DIFFUSION, HANGING DROP, temperature 283K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BSRF / Beamline: 3W1A / Wavelength: 0.98 Å
DetectorDetector: CCD / Date: Jan 28, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.816→80.582 Å / Num. obs: 7694 / Redundancy: 8.4 % / Rmerge(I) obs: 0.063
Reflection shellResolution: 2.816→2.92 Å

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
AUTOMARdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3B4D

3b4d


Resolution: 2.82→80.58 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.862 / SU B: 18.953 / SU ML: 0.378 / Cross valid method: THROUGHOUT / ESU R Free: 0.481 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2897 354 4.6 %RANDOM
Rwork0.22631 ---
obs0.22932 7338 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.295 Å2
Baniso -1Baniso -2Baniso -3
1-1.1 Å20.55 Å20 Å2
2--1.1 Å20 Å2
3----1.65 Å2
Refinement stepCycle: LAST / Resolution: 2.82→80.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2489 0 0 33 2522
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0212487
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2521.9463356
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9665315
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.99122.522115
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.84415393
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.0391521
X-RAY DIFFRACTIONr_chiral_restr0.0770.2367
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021921
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2080.21001
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3050.21695
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1730.295
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1770.245
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.270.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.651.51608
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.98922502
X-RAY DIFFRACTIONr_scbond_it1.3943949
X-RAY DIFFRACTIONr_scangle_it2.1114.5854
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.816→2.889 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.534 34 -
Rwork0.324 532 -
obs--100 %

+
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