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- PDB-6a6j: Crystal structure of Zebra fish Y-box protein1 (YB-1) Cold-shock ... -

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Basic information

Entry
Database: PDB / ID: 6a6j
TitleCrystal structure of Zebra fish Y-box protein1 (YB-1) Cold-shock domain in complex with 6mer m5C RNA
Components
  • RNA (5'-R(P*CP*AP*UP*(5MC)P*U)-3')
  • Zebra fish Y-box protein1 (YB-1)
KeywordsRNA BINDING PROTEIN/RNA / OB-fold / RNA BINDING PROTEIN-RNA complex
Function / homology
Function and homology information


negative regulation of mRNA processing / mRNA Splicing - Major Pathway / : / establishment of RNA localization / : / tRNA transport / CRD-mediated mRNA stability complex / C5-methylcytidine-containing RNA reader activity / miRNA transport / negative regulation of striated muscle cell differentiation ...negative regulation of mRNA processing / mRNA Splicing - Major Pathway / : / establishment of RNA localization / : / tRNA transport / CRD-mediated mRNA stability complex / C5-methylcytidine-containing RNA reader activity / miRNA transport / negative regulation of striated muscle cell differentiation / RNA transport / Noncanonical activation of NOTCH3 / negative regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / messenger ribonucleoprotein complex / CRD-mediated mRNA stabilization / protein localization to cytoplasmic stress granule / eukaryotic initiation factor 4E binding / histone pre-mRNA 3'end processing complex / embryonic morphogenesis / U12-type spliceosomal complex / positive regulation of cytoplasmic translation / mRNA stabilization / cellular response to interleukin-7 / miRNA binding / mRNA Splicing - Minor Pathway / negative regulation of cellular senescence / negative regulation of mRNA splicing, via spliceosome / Processing of Capped Intron-Containing Pre-mRNA / positive regulation of cell division / epidermis development / negative regulation of translational initiation / mRNA Splicing - Major Pathway / RNA splicing / P-body / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / mRNA processing / cytoplasmic stress granule / Interferon gamma signaling / sequence-specific double-stranded DNA binding / single-stranded DNA binding / GTPase binding / double-stranded DNA binding / regulation of gene expression / in utero embryonic development / negative regulation of translation / nucleic acid binding / ribonucleoprotein complex / mRNA binding / intracellular membrane-bounded organelle / synapse / chromatin binding / regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / positive regulation of transcription by RNA polymerase II / DNA binding / RNA binding / extracellular exosome / extracellular region / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Cold-shock (CSD) domain / Cold-shock (CSD) domain signature. / Cold-shock (CSD) domain profile. / Cold-shock protein, DNA-binding / 'Cold-shock' DNA-binding domain / Cold shock domain / Cold shock protein domain / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold ...Cold-shock (CSD) domain / Cold-shock (CSD) domain signature. / Cold-shock (CSD) domain profile. / Cold-shock protein, DNA-binding / 'Cold-shock' DNA-binding domain / Cold shock domain / Cold shock protein domain / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
RNA / Y-box-binding protein 1 / Y-box-binding protein 1
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.255 Å
AuthorsZhang, M.M. / Wu, B.X. / Huang, Y. / Ma, J.B.
CitationJournal: Mol.Cell / Year: 2019
Title: RNA 5-Methylcytosine Facilitates the Maternal-to-Zygotic Transition by Preventing Maternal mRNA Decay.
Authors: Yang, Y. / Wang, L. / Han, X. / Yang, W.L. / Zhang, M. / Ma, H.L. / Sun, B.F. / Li, A. / Xia, J. / Chen, J. / Heng, J. / Wu, B. / Chen, Y.S. / Xu, J.W. / Yang, X. / Yao, H. / Sun, J. / Lyu, ...Authors: Yang, Y. / Wang, L. / Han, X. / Yang, W.L. / Zhang, M. / Ma, H.L. / Sun, B.F. / Li, A. / Xia, J. / Chen, J. / Heng, J. / Wu, B. / Chen, Y.S. / Xu, J.W. / Yang, X. / Yao, H. / Sun, J. / Lyu, C. / Wang, H.L. / Huang, Y. / Sun, Y.P. / Zhao, Y.L. / Meng, A. / Ma, J. / Liu, F. / Yang, Y.G.
History
DepositionJun 28, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 19, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2019Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / struct_ref / struct_ref_seq
Item: _entity.pdbx_description / _entity.pdbx_fragment ..._entity.pdbx_description / _entity.pdbx_fragment / _entity_name_com.name / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_db_accession
Revision 1.2Aug 14, 2019Group: Data collection / Database references / Structure summary
Category: audit_author / citation / citation_author
Item: _audit_author.name / _citation.country ..._audit_author.name / _citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.3Aug 21, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.4Oct 2, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.5Mar 27, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Zebra fish Y-box protein1 (YB-1)
B: RNA (5'-R(P*CP*AP*UP*(5MC)P*U)-3')
C: Zebra fish Y-box protein1 (YB-1)
D: RNA (5'-R(P*CP*AP*UP*(5MC)P*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0406
Polymers23,9094
Non-polymers1312
Water91951
1
A: Zebra fish Y-box protein1 (YB-1)
B: RNA (5'-R(P*CP*AP*UP*(5MC)P*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,0203
Polymers11,9542
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1790 Å2
ΔGint-39 kcal/mol
Surface area5780 Å2
MethodPISA
2
C: Zebra fish Y-box protein1 (YB-1)
D: RNA (5'-R(P*CP*AP*UP*(5MC)P*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,0203
Polymers11,9542
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1790 Å2
ΔGint-41 kcal/mol
Surface area5770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.201, 60.866, 56.513
Angle α, β, γ (deg.)90.00, 118.97, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Zebra fish Y-box protein1 (YB-1) / Ybx1 protein


Mass: 10127.321 Da / Num. of mol.: 2 / Fragment: cold-shock domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: ybx1 / Production host: Escherichia coli (E. coli) / References: UniProt: B5DE31, UniProt: P67809*PLUS
#2: RNA chain RNA (5'-R(P*CP*AP*UP*(5MC)P*U)-3')


Mass: 1827.135 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 51 / 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: 1

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Sample preparation

CrystalDensity Matthews: 1.96 Å3/Da / Density % sol: 37.16 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / Details: 0.05M Zinc acetate, 22% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97914 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 19, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97914 Å / Relative weight: 1
ReflectionResolution: 2.25→30 Å / Num. obs: 7519 / % possible obs: 94.6 % / Redundancy: 6.3 % / Net I/σ(I): 7.38
Reflection shellResolution: 2.25→2.33 Å

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementResolution: 2.255→27.21 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 30.46
RfactorNum. reflection% reflection
Rfree0.2724 754 10.03 %
Rwork0.2247 --
obs0.2295 7519 44.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.255→27.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1386 206 2 51 1645
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041636
X-RAY DIFFRACTIONf_angle_d1.1332248
X-RAY DIFFRACTIONf_dihedral_angle_d16.12620
X-RAY DIFFRACTIONf_chiral_restr0.131254
X-RAY DIFFRACTIONf_plane_restr0.003262
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.255-2.4290.29651070.2691931X-RAY DIFFRACTION30
2.429-2.67330.3611600.27061337X-RAY DIFFRACTION44
2.6733-3.05960.31161560.25121536X-RAY DIFFRACTION49
3.0596-3.85310.28521630.21811468X-RAY DIFFRACTION48
3.8531-27.21150.2221680.19881493X-RAY DIFFRACTION49

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