[English] 日本語
Yorodumi
- PDB-3zzy: Crystal structure of a Raver1 PRI3 peptide in complex with polypy... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3zzy
TitleCrystal structure of a Raver1 PRI3 peptide in complex with polypyrimidine tract binding protein RRM2
Components
  • POLYPYRIMIDINE TRACT-BINDING PROTEIN 1
  • RIBONUCLEOPROTEIN PTB-BINDING 1
KeywordsPROTEIN BINDING / PEPTIDE BINDING / RNA RECOGNITION MOTIF
Function / homology
Function and homology information


negative regulation of muscle cell differentiation / poly-pyrimidine tract binding / IRES-dependent viral translational initiation / positive regulation of calcineurin-NFAT signaling cascade / pre-mRNA binding / negative regulation of RNA splicing / FGFR2 alternative splicing / negative regulation of neuron differentiation / regulation of alternative mRNA splicing, via spliceosome / regulation of RNA splicing ...negative regulation of muscle cell differentiation / poly-pyrimidine tract binding / IRES-dependent viral translational initiation / positive regulation of calcineurin-NFAT signaling cascade / pre-mRNA binding / negative regulation of RNA splicing / FGFR2 alternative splicing / negative regulation of neuron differentiation / regulation of alternative mRNA splicing, via spliceosome / regulation of RNA splicing / negative regulation of mRNA splicing, via spliceosome / regulation of cell differentiation / Processing of Capped Intron-Containing Pre-mRNA / neurogenesis / mRNA Splicing - Major Pathway / RNA splicing / mRNA processing / mRNA binding / nucleolus / positive regulation of transcription by RNA polymerase II / RNA binding / extracellular exosome / nucleoplasm / nucleus / membrane / cytoplasm
Similarity search - Function
Ribonucleoprotein PTB-binding 1, RNA recognition motif 1 / PTBP1, RNA recognition motif 1 / PTBP1, RNA recognition motif 3 / HnRNP-L/PTB / PTBP1-like, RNA recognition motif 2 / RRM-like domain / : / RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) / RRM (RNA recognition motif) domain / RNA recognition motif ...Ribonucleoprotein PTB-binding 1, RNA recognition motif 1 / PTBP1, RNA recognition motif 1 / PTBP1, RNA recognition motif 3 / HnRNP-L/PTB / PTBP1-like, RNA recognition motif 2 / RRM-like domain / : / RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) / 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
Polypyrimidine tract-binding protein 1 / Ribonucleoprotein PTB-binding 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsJoshi, A. / Kotik-Kogan, O. / Curry, S.
CitationJournal: Structure / Year: 2011
Title: Crystallographic Analysis of Polypyrimidine Tract-Binding Protein-Raver1 Interactions Involved in Regulation of Alternative Splicing.
Authors: Joshi, A. / Coelho, M.B. / Kotik-Kogan, O. / Simpson, P.J. / Matthews, S.J. / Smith, C.W. / Curry, S.
History
DepositionSep 6, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 28, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: POLYPYRIMIDINE TRACT-BINDING PROTEIN 1
B: POLYPYRIMIDINE TRACT-BINDING PROTEIN 1
C: RIBONUCLEOPROTEIN PTB-BINDING 1
D: RIBONUCLEOPROTEIN PTB-BINDING 1


Theoretical massNumber of molelcules
Total (without water)31,2744
Polymers31,2744
Non-polymers00
Water3,441191
1
A: POLYPYRIMIDINE TRACT-BINDING PROTEIN 1
C: RIBONUCLEOPROTEIN PTB-BINDING 1


Theoretical massNumber of molelcules
Total (without water)15,6372
Polymers15,6372
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area860 Å2
ΔGint-6.5 kcal/mol
Surface area6260 Å2
MethodPISA
2
B: POLYPYRIMIDINE TRACT-BINDING PROTEIN 1
D: RIBONUCLEOPROTEIN PTB-BINDING 1


Theoretical massNumber of molelcules
Total (without water)15,6372
Polymers15,6372
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area830 Å2
ΔGint-6.5 kcal/mol
Surface area6130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.233, 60.606, 60.842
Angle α, β, γ (deg.)90.00, 107.51, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.2051, 0.0424, 0.9778), (-0.02532, -0.999, 0.038), (0.9784, -0.01697, 0.2059)
Vector: -47.02, -10.24, 16.62)

-
Components

#1: Protein POLYPYRIMIDINE TRACT-BINDING PROTEIN 1 / PTB / 57 KDA RNA-BINDING PROTEIN PPTB-1 / HETEROGENEOUS NUCLEAR RIBONUCLEOPROTEIN I / HNRNP I


Mass: 14169.072 Da / Num. of mol.: 2 / Fragment: RNA RECOGNITION MOTIF 2, RESIDUES 172-301
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P26599
#2: Protein/peptide RIBONUCLEOPROTEIN PTB-BINDING 1 / RAVER1 / PROTEIN RAVER-1


Mass: 1467.710 Da / Num. of mol.: 2 / Fragment: MOTIF PRI3, RESIDUES 496-507 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: THIS FRAGMENT IS ACTUALLY FUSED TO MOLECULE 1, SEE REMARK 999
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9CW46
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 191 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsCHAIN C AND D FIRST 4 RESIDUES (GAMG) ARE VECTOR DERIVED. RESIDUES 5 - 16 CORRESPOND TO RAVER1 PRI3 ...CHAIN C AND D FIRST 4 RESIDUES (GAMG) ARE VECTOR DERIVED. RESIDUES 5 - 16 CORRESPOND TO RAVER1 PRI3 MOTIF. THESE 16 RESIDUES ARE FUSED GENETICALLY TO PTB RRM2 ( RECORDED AS CHAINS A AND B). BECAUSE OF LINKER DISORDER WE CANNOT DETERMINE WHICH RRM DOMAIN (CHAINS A, B) IS COVALENTLY LINKED TO WHICH RAVER1 PEPTIDE (CHAINS C,D). METHIONINE 1 IN RAVER1 IS AN INITIATOR MET AND IS REMOVED.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.01 Å3/Da / Density % sol: 38.94 % / Description: NONE
Crystal growpH: 6.5 / Details: SEE PAPER., pH 6.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.8123
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 15, 2008 / Details: MIRROR
RadiationMonochromator: GEMANIUM CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8123 Å / Relative weight: 1
ReflectionResolution: 1.4→30.32 Å / Num. obs: 50129 / % possible obs: 98.9 % / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Biso Wilson estimate: 19.5 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 15.4
Reflection shellResolution: 1.4→1.48 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 5.3 / % possible all: 96.1

-
Processing

Software
NameVersionClassification
CNS1.2refinement
MOSFLMdata reduction
SCALAdata scaling
PHASER1.3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1SJR

1sjr


Resolution: 1.4→29.01 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 839936.87 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MLF
Details: BULK SOLVENT MODEL USED. THE CRYSTALLISED PROTEIN HAS A RAVER1 PEPTIDE GENETICALLY FUSED AS AN N-TERMINAL EXTENSION OF PTB RRM2. OWING TO LINKER DISORDER WE CANNOT DETERMINE WHICH RRM DOMAIN ...Details: BULK SOLVENT MODEL USED. THE CRYSTALLISED PROTEIN HAS A RAVER1 PEPTIDE GENETICALLY FUSED AS AN N-TERMINAL EXTENSION OF PTB RRM2. OWING TO LINKER DISORDER WE CANNOT DETERMINE WHICH RRM DOMAIN (CHAINS A, B) IS COVALENTLY LINKED TO WHICH RAVER1 PEPTIDE (CHAINS C,D).
RfactorNum. reflection% reflectionSelection details
Rfree0.234 2506 5 %RANDOM
Rwork0.224 ---
obs0.224 50129 98.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 63.17 Å2 / ksol: 0.45 e/Å3
Displacement parametersBiso mean: 22.1 Å2
Baniso -1Baniso -2Baniso -3
1-2.22 Å20 Å2-5.57 Å2
2---5.39 Å20 Å2
3---3.17 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 1.4→29.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1741 0 0 191 1932
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.76
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 1.4→1.49 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.313 411 5 %
Rwork0.325 7750 -
obs--97.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAMWATER.TOP

+
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