[English] 日本語
Yorodumi
- PDB-3kuj: Crystal structure of C-terminal domain of PABPC1 in complex with ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3kuj
TitleCrystal structure of C-terminal domain of PABPC1 in complex with binding region of eRF3a
Components
  • GSPT1 protein
  • Polyadenylate-binding protein 1
KeywordsPROTEIN BINDING / protein-protein complex / Methylation / mRNA processing / mRNA splicing / Nucleus / Phosphoprotein / RNA-binding / Spliceosome / GTP-binding / Nucleotide-binding
Function / homology
Function and homology information


gamma-glutamyltransferase / glutathione gamma-glutamate hydrolase / glutathione hydrolase activity / leukotriene C4 gamma-glutamyl transferase activity / translation release factor complex / glutathione catabolic process / translation release factor activity / regulation of translational termination / glutathione biosynthetic process / protein methylation ...gamma-glutamyltransferase / glutathione gamma-glutamate hydrolase / glutathione hydrolase activity / leukotriene C4 gamma-glutamyl transferase activity / translation release factor complex / glutathione catabolic process / translation release factor activity / regulation of translational termination / glutathione biosynthetic process / protein methylation / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / Eukaryotic Translation Termination / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / cytosolic ribosome / translational termination / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / Regulation of expression of SLITs and ROBOs / G1/S transition of mitotic cell cycle / translation / cell cycle / GTPase activity / GTP binding / RNA binding / metal ion binding / cytoplasm / cytosol
Similarity search - Function
Ataxin-2, C-terminal / Ataxin-2 C-terminal region / c-terminal domain of poly(a) binding protein / c-terminal domain of poly(a) binding protein / Poly-adenylate binding protein, unique domain / Gamma-glutamyltranspeptidase / Gamma-glutamyltranspeptidase signature. / Gamma-glutamyltranspeptidase / Gamma-glutamyltranspeptidase, large subunit, C-terminal domain / Gamma-glutamyltranspeptidase, small subunit ...Ataxin-2, C-terminal / Ataxin-2 C-terminal region / c-terminal domain of poly(a) binding protein / c-terminal domain of poly(a) binding protein / Poly-adenylate binding protein, unique domain / Gamma-glutamyltranspeptidase / Gamma-glutamyltranspeptidase signature. / Gamma-glutamyltranspeptidase / Gamma-glutamyltranspeptidase, large subunit, C-terminal domain / Gamma-glutamyltranspeptidase, small subunit / Translation elongation factor EFTu/EF1A, C-terminal / Elongation factor Tu C-terminal domain / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / Tr-type G domain, conserved site / Translational (tr)-type guanine nucleotide-binding (G) domain signature. / Translation elongation factor EFTu-like, domain 2 / Elongation factor Tu domain 2 / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / Nucleophile aminohydrolases, N-terminal / Prokaryotic membrane lipoprotein lipid attachment site profile. / Translation protein, beta-barrel domain superfamily / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Glutathione hydrolase proenzyme / Eukaryotic peptide chain release factor GTP-binding subunit ERF3B / Eukaryotic peptide chain release factor GTP-binding subunit ERF3A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsKozlov, G. / Gehring, K.
CitationJournal: Plos One / Year: 2010
Title: Molecular basis of eRF3 recognition by the MLLE domain of poly(A)-binding protein.
Authors: Kozlov, G. / Gehring, K.
History
DepositionNov 27, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 12, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Sep 6, 2023Group: 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_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_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: Polyadenylate-binding protein 1
B: GSPT1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,2894
Polymers11,0972
Non-polymers1922
Water95553
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1630 Å2
ΔGint-35 kcal/mol
Surface area5690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.217, 50.802, 32.121
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein Polyadenylate-binding protein 1 / Poly(A)-binding protein 1 / PABP 1


Mass: 9421.909 Da / Num. of mol.: 1 / Fragment: C-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PABPC1, PAB1, PABP1, PABPC2 / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P11940
#2: Protein/peptide GSPT1 protein


Mass: 1674.913 Da / Num. of mol.: 1 / Fragment: PABPC1-binding region / Source method: obtained synthetically / Details: chemically synthesized / Source: (synth.) Homo sapiens (human) / References: UniProt: Q96GF2, UniProt: Q8IYD1*PLUS
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 1.66 Å3/Da / Density % sol: 26.01 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 1.4M ammonium sulfate, 0.1M citric acid, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F2 / Wavelength: 0.978 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 29, 2008 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. all: 14288 / Num. obs: 14231 / % possible obs: 99.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 7.5 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 19.2
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.375 / Mean I/σ(I) obs: 6.1 / Num. unique all: 997 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1I2T

1i2t


Resolution: 1.4→33.77 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.935 / SU B: 1.865 / SU ML: 0.039 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.074 / ESU R Free: 0.074 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.22331 756 5 %RANDOM
Rwork0.19578 ---
obs0.19713 14231 99.36 %-
all-14288 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.223 Å2
Baniso -1Baniso -2Baniso -3
1-0.2 Å20 Å20 Å2
2---0.21 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.4→33.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms698 0 10 53 761
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.022729
X-RAY DIFFRACTIONr_angle_refined_deg1.2492.007992
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.037594
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.18525.92627
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.25115129
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.126152
X-RAY DIFFRACTIONr_chiral_restr0.1060.2118
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02523
X-RAY DIFFRACTIONr_nbd_refined0.2090.2322
X-RAY DIFFRACTIONr_nbtor_refined0.3040.2502
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0730.232
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2150.255
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.180.212
X-RAY DIFFRACTIONr_mcbond_it0.6621.5477
X-RAY DIFFRACTIONr_mcangle_it1.0132757
X-RAY DIFFRACTIONr_scbond_it1.9453263
X-RAY DIFFRACTIONr_scangle_it2.864.5233
LS refinement shellResolution: 1.4→1.438 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.205 49 -
Rwork0.218 997 -
obs--96.32 %
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)
121.2737-2.37094.50066.12071.3378.4661-0.28230.2376-0.0071-0.13610.0878-0.0288-0.45860.04840.19460.0766-0.0458-0.0299-0.01540.0081-0.071410.304412.298819.1186
25.69461.66582.26684.5252.36664.09270.0126-0.2426-0.02970.13450.07310.0824-0.09970.2377-0.08570.0629-0.039-0.0210.0610.007-0.012411.41026.265513.6167
30.88150.77460.11472.36910.60110.70730.0158-0.0118-0.06130.0028-0.0356-0.0744-0.00530.00680.01980.0225-0.0058-0.00280.03070.00260.03628.93685.24843.6889
46.0592-1.5579-4.80882.09042.51317.9221-0.05340.0969-0.1638-0.0949-0.00260.0180.1770.04940.0560.0470.0002-0.00140.01830.00930.03377.6936.0921-4.2272
53.8411-3.9714.79411.0162-9.08299.58150.028-0.11-0.2191-0.1350.00980.0020.07680.0515-0.0379-0.00070.00370.01440.03420.0030.057217.3117.7562-1.9525
61.5729-1.912-4.400240.3717-34.722154.512-0.66010.03560.3091.39870.5024-0.24770.5735-0.77520.15770.07520.0061-0.0641-0.0250.0343-0.03713.8192-3.50512.0592
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A544 - 556
2X-RAY DIFFRACTION2A557 - 566
3X-RAY DIFFRACTION3A567 - 596
4X-RAY DIFFRACTION4A597 - 620
5X-RAY DIFFRACTION5B76 - 84
6X-RAY DIFFRACTION6B85 - 90

+
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://pdbjlvh1.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