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- PDB-1cvj: X-RAY CRYSTAL STRUCTURE OF THE POLY(A)-BINDING PROTEIN IN COMPLEX... -

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Basic information

Entry
Database: PDB / ID: 1cvj
TitleX-RAY CRYSTAL STRUCTURE OF THE POLY(A)-BINDING PROTEIN IN COMPLEX WITH POLYADENYLATE RNA
Components
  • 5'-R(*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3'
  • POLYADENYLATE BINDING PROTEIN 1
KeywordsGENE REGULATION/RNA / RRM / PROTEIN-RNA COMPLEX / GENE REGULATION-RNA COMPLEX
Function / homology
Function and homology information


mCRD-mediated mRNA stability complex / negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / translation activator activity / negative regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / CRD-mediated mRNA stabilization / Z-decay: degradation of maternal mRNAs by zygotically expressed factors / Deadenylation of mRNA / positive regulation of cytoplasmic translation / M-decay: degradation of maternal mRNAs by maternally stored factors / poly(A) binding ...mCRD-mediated mRNA stability complex / negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / translation activator activity / negative regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / CRD-mediated mRNA stabilization / Z-decay: degradation of maternal mRNAs by zygotically expressed factors / Deadenylation of mRNA / positive regulation of cytoplasmic translation / M-decay: degradation of maternal mRNAs by maternally stored factors / poly(A) binding / regulatory ncRNA-mediated gene silencing / mRNA stabilization / poly(U) RNA binding / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / Translation initiation complex formation / cell leading edge / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / L13a-mediated translational silencing of Ceruloplasmin expression / positive regulation of viral genome replication / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / catalytic step 2 spliceosome / mRNA 3'-UTR binding / AUF1 (hnRNP D0) binds and destabilizes mRNA / mRNA splicing, via spliceosome / Regulation of expression of SLITs and ROBOs / cytoplasmic ribonucleoprotein granule / cytoplasmic stress granule / lamellipodium / ribonucleoprotein complex / focal adhesion / mRNA binding / RNA binding / extracellular exosome / membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
: / PABP, RNA recognition motif 2 / Polyadenylate binding protein, human types 1, 2, 3, 4 / Poly(A)-binding protein C-terminal (PABC) domain profile. / C-terminal domain of Poly(A)-binding protein. Present also in Drosophila hyperplastics discs protein. / Polyadenylate-binding protein/Hyperplastic disc protein / PABC (PABP) domain / Poly-adenylate binding protein, unique domain / RNA recognition motif domain, eukaryote / RNA recognition motif ...: / PABP, RNA recognition motif 2 / Polyadenylate binding protein, human types 1, 2, 3, 4 / Poly(A)-binding protein C-terminal (PABC) domain profile. / C-terminal domain of Poly(A)-binding protein. Present also in Drosophila hyperplastics discs protein. / Polyadenylate-binding protein/Hyperplastic disc protein / PABC (PABP) domain / Poly-adenylate binding protein, unique domain / RNA recognition motif domain, eukaryote / RNA recognition motif / 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
ADENOSINE MONOPHOSPHATE / RNA / RNA (> 10) / Polyadenylate-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.6 Å
AuthorsDeo, R.C. / Bonanno, J.B. / Sonenberg, N. / Burley, S.K.
CitationJournal: Cell(Cambridge,Mass.) / Year: 1999
Title: Recognition of polyadenylate RNA by the poly(A)-binding protein.
Authors: Deo, R.C. / Bonanno, J.B. / Sonenberg, N. / Burley, S.K.
History
DepositionAug 23, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 4, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 3, 2021Group: Advisory / Database references ...Advisory / Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / pdbx_unobs_or_zero_occ_atoms / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 7, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.0May 29, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_unobs_or_zero_occ_atoms / struct_site
Item: _atom_site.auth_comp_id / _atom_site.label_comp_id ..._atom_site.auth_comp_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_unobs_or_zero_occ_atoms.auth_atom_id / _pdbx_unobs_or_zero_occ_atoms.auth_comp_id / _pdbx_unobs_or_zero_occ_atoms.label_atom_id / _pdbx_unobs_or_zero_occ_atoms.label_comp_id / _struct_site.details / _struct_site.pdbx_auth_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
M: 5'-R(*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3'
N: 5'-R(*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3'
O: 5'-R(*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3'
P: 5'-R(*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3'
Q: 5'-R(*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3'
R: 5'-R(*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3'
S: 5'-R(*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3'
T: 5'-R(*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3'
A: POLYADENYLATE BINDING PROTEIN 1
B: POLYADENYLATE BINDING PROTEIN 1
C: POLYADENYLATE BINDING PROTEIN 1
D: POLYADENYLATE BINDING PROTEIN 1
E: POLYADENYLATE BINDING PROTEIN 1
F: POLYADENYLATE BINDING PROTEIN 1
G: POLYADENYLATE BINDING PROTEIN 1
H: POLYADENYLATE BINDING PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)203,09724
Polymers200,31916
Non-polymers2,7788
Water95553
1
M: 5'-R(*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3'
A: POLYADENYLATE BINDING PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3873
Polymers25,0402
Non-polymers3471
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
N: 5'-R(*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3'
B: POLYADENYLATE BINDING PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3873
Polymers25,0402
Non-polymers3471
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
O: 5'-R(*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3'
C: POLYADENYLATE BINDING PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3873
Polymers25,0402
Non-polymers3471
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
P: 5'-R(*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3'
D: POLYADENYLATE BINDING PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3873
Polymers25,0402
Non-polymers3471
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
Q: 5'-R(*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3'
E: POLYADENYLATE BINDING PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3873
Polymers25,0402
Non-polymers3471
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
R: 5'-R(*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3'
F: POLYADENYLATE BINDING PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3873
Polymers25,0402
Non-polymers3471
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
S: 5'-R(*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3'
G: POLYADENYLATE BINDING PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3873
Polymers25,0402
Non-polymers3471
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
T: 5'-R(*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3'
H: POLYADENYLATE BINDING PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3873
Polymers25,0402
Non-polymers3471
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.557, 176.797, 82.489
Angle α, β, γ (deg.)90.00, 117.67, 90.00
Int Tables number4
Cell settingmonoclinic
Space group name H-MP1211

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Components

#1: RNA chain
5'-R(*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3'


Mass: 3576.306 Da / Num. of mol.: 8 / Source method: obtained synthetically
#2: Protein
POLYADENYLATE BINDING PROTEIN 1 / POLY(A) BINDING PROTEIN 1 / PABP 1


Mass: 21463.604 Da / Num. of mol.: 8 / Fragment: RESIDUES 1-190
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PGEX6P1 / Production host: Escherichia coli (E. coli) / References: UniProt: P11940
#3: Chemical
ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.56 Å3/Da / Density % sol: 52.03 %
Crystal growTemperature: 296.7 K / Method: vapor diffusion, hanging drop / pH: 8
Details: AMMONIUM SULFATE, TCEP, TRIS-HCL, POTASSIUM CHLORIDE, GLYCEROL, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 296.7K
Components of the solutions
IDNameCrystal-IDSol-ID
1TCEP11
2TRIS-HCL11
3KCL11
4(NH4)SO411
5GLYCEROL11
6(NH4)SO412
7GLYCEROL12
Crystal grow
*PLUS
Temperature: 24 ℃ / Details: a 1 : 1.2 protein : RNA ratio
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
12.1 Mammonium sulfate1reservoir
2100 mMTris-HCl1reservoirpH8.0
35.5 mg/mlprotein1drop
4RNA1drop
51
61
71

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
1931
2931
3931
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONCHESS A110.935
SYNCHROTRONCHESS F120.9159
SYNCHROTRONNSLS X9B30.9771
Detector
TypeIDDetectorDate
OTHER1CCDDec 11, 1998
OTHER2CCDFeb 3, 1999
OTHER3CCDFeb 22, 1999
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
3SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.9351
20.91591
30.97711
ReflectionResolution: 2.6→20 Å / Num. all: 61125 / Num. obs: 61125 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 60 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 19
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 3 % / Rmerge(I) obs: 0.294 / % possible all: 99.7
Reflection
*PLUS

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Processing

Software
NameClassification
MLPHAREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.6→20 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.304 5791 10 %RANDOM
Rwork0.23 ---
obs0.23 57149 --
all-61739 --
Refinement stepCycle: LAST / Resolution: 2.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9683 1274 152 53 11162
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d1.57
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
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
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 20 Å / σ(F): 2 / % reflection Rfree: 10 % / Rfactor obs: 0.23 / Rfactor Rwork: 0.23
Solvent computation
*PLUS
Displacement parameters
*PLUS

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