[English] 日本語
Yorodumi
- PDB-7bn3: Crystal structure of C-terminal domain of PABPC1 in complex with ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7bn3
TitleCrystal structure of C-terminal domain of PABPC1 in complex with Nucleoprotein from Human Coronavirus 229E
Components
  • Isoform 2 of Polyadenylate-binding protein 1
  • Nucleoprotein from Human Coronavirus 229E
KeywordsTRANSCRIPTION / PABPC1 / RNA binding / Nucleoprotein / Human coronavirus 229E
Function / homology
Function and homology information


mCRD-mediated mRNA stability complex / negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / negative regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / CRD-mediated mRNA stabilization / translation activator activity / Z-decay: degradation of maternal mRNAs by zygotically expressed factors / Deadenylation of mRNA / poly(A) binding / M-decay: degradation of maternal mRNAs by maternally stored factors / positive regulation of cytoplasmic translation ...mCRD-mediated mRNA stability complex / negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / negative regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / CRD-mediated mRNA stabilization / translation activator activity / Z-decay: degradation of maternal mRNAs by zygotically expressed factors / Deadenylation of mRNA / poly(A) binding / M-decay: degradation of maternal mRNAs by maternally stored factors / positive regulation of cytoplasmic translation / regulatory ncRNA-mediated gene silencing / mRNA stabilization / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / poly(U) RNA binding / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / Translation initiation complex formation / cell leading edge / 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 / nucleus / membrane / cytoplasm / cytosol
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 / MLLE 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 / MLLE domain / RNA recognition motif domain, eukaryote / RNA recognition motif / 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
Similarity search - Domain/homology
Polyadenylate-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Human coronavirus 229E
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsBadgujar, D.C. / Dobritzsch, D.
Funding support Sweden, 3items
OrganizationGrant numberCountry
The Swedish Foundation for Strategic ResearchSB16-0039 Sweden
Swedish Research Council2016-04965 Sweden
Swedish Research Council2016-04134 Sweden
CitationJournal: Nat Commun / Year: 2023
Title: Large-scale phage-based screening reveals extensive pan-viral mimicry of host short linear motifs
Authors: Mihalic, F. / Simonetti, L. / Giudice, G. / Sander, M.R. / Lindqvist, R. / Peters, M.B.A. / Benz, C. / Kassa, E. / Badgujar, D. / Inturi, R. / Ali, M. / Krystkowiak, I. / Sayadi, A. / ...Authors: Mihalic, F. / Simonetti, L. / Giudice, G. / Sander, M.R. / Lindqvist, R. / Peters, M.B.A. / Benz, C. / Kassa, E. / Badgujar, D. / Inturi, R. / Ali, M. / Krystkowiak, I. / Sayadi, A. / Andersson, E. / Aronsson, H. / Soderberg, O. / Dobritzsch, D. / Petsalaki, E. / Overby, A.K. / Jemth, P. / Davey, N.E. / Ivarsson, Y.
History
DepositionJan 21, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.1May 10, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Isoform 2 of Polyadenylate-binding protein 1
B: Isoform 2 of Polyadenylate-binding protein 1
C: Isoform 2 of Polyadenylate-binding protein 1
F: Nucleoprotein from Human Coronavirus 229E
D: Nucleoprotein from Human Coronavirus 229E
E: Nucleoprotein from Human Coronavirus 229E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,07610
Polymers34,6966
Non-polymers3804
Water1,42379
1
A: Isoform 2 of Polyadenylate-binding protein 1
D: Nucleoprotein from Human Coronavirus 229E


Theoretical massNumber of molelcules
Total (without water)11,5652
Polymers11,5652
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1390 Å2
ΔGint-11 kcal/mol
Surface area6040 Å2
MethodPISA
2
B: Isoform 2 of Polyadenylate-binding protein 1
E: Nucleoprotein from Human Coronavirus 229E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,8495
Polymers11,5652
Non-polymers2843
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1440 Å2
ΔGint-23 kcal/mol
Surface area6090 Å2
MethodPISA
3
C: Isoform 2 of Polyadenylate-binding protein 1
F: Nucleoprotein from Human Coronavirus 229E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,6613
Polymers11,5652
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1420 Å2
ΔGint-23 kcal/mol
Surface area5880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.509, 150.065, 65.502
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C
14F
24D
15F
25E
16D
26E

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALAAA544 - 62610 - 92
21ALAALABB544 - 62610 - 92
12ALAALAAA544 - 62610 - 92
22ALAALACC544 - 62610 - 92
13ALAALABB544 - 62610 - 92
23ALAALACC544 - 62610 - 92
14PROPROFD2 - 132 - 13
24PROPRODE2 - 132 - 13
15ASNASNFD2 - 122 - 12
25ASNASNEF2 - 122 - 12
16ASNASNDE2 - 122 - 12
26ASNASNEF2 - 122 - 12

NCS ensembles :
ID
1
2
3
4
5
6

-
Components

#1: Protein Isoform 2 of Polyadenylate-binding protein 1 / Poly(A)-binding protein 1


Mass: 9636.063 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PABPC1, PAB1, PABP1, PABPC2 / Production host: Escherichia coli (E. coli) / References: UniProt: P11940
#2: Protein/peptide Nucleoprotein from Human Coronavirus 229E


Mass: 1929.113 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Human coronavirus 229E
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.25 Å3/Da / Density % sol: 45.31 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M MES sodium salt pH-6.5, 1.8 M Ammonium Sulfate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 1.003 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 28, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.003 Å / Relative weight: 1
ReflectionResolution: 1.93→43.63 Å / Num. obs: 23731 / % possible obs: 99.1 % / Redundancy: 13.2 % / CC1/2: 0.999 / Net I/σ(I): 12.7
Reflection shellResolution: 1.93→2 Å / Num. unique obs: 2268 / CC1/2: 0.999

-
Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3kuj

3kuj


Resolution: 1.93→39.3 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.949 / SU B: 3.893 / SU ML: 0.108 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.155 / ESU R Free: 0.142 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2277 1125 4.7 %RANDOM
Rwork0.1931 ---
obs0.1949 22588 98.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 134.57 Å2 / Biso mean: 49.752 Å2 / Biso min: 33.95 Å2
Baniso -1Baniso -2Baniso -3
1-0.27 Å20 Å20 Å2
2---0.31 Å20 Å2
3---0.04 Å2
Refinement stepCycle: final / Resolution: 1.93→39.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2142 0 21 79 2242
Biso mean--72.58 55.04 -
Num. residues----286
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0132207
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172135
X-RAY DIFFRACTIONr_angle_refined_deg1.4491.6442991
X-RAY DIFFRACTIONr_angle_other_deg1.3651.5624994
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8895282
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.48925.16989
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.24315388
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.273157
X-RAY DIFFRACTIONr_chiral_restr0.0820.2296
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022397
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02344
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A23800.09
12B23800.09
21A23840.09
22C23840.09
31B23830.1
32C23830.1
41F2470.19
42D2470.19
51F2300.11
52E2300.11
61D2300.14
62E2300.14
LS refinement shellResolution: 1.93→1.98 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 70 -
Rwork0.296 1629 -
all-1699 -
obs--98.09 %

+
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