[English] 日本語
Yorodumi
- PDB-7z89: Sam68 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7z89
TitleSam68
ComponentsIsoform 2 of KH domain-containing, RNA-binding, signal transduction-associated protein 1
KeywordsRNA BINDING PROTEIN / Spinal muscular Atrophy
Function / homology
Function and homology information


regulation of RNA export from nucleus / Grb2-Sos complex / PTK6 Regulates Proteins Involved in RNA Processing / positive regulation of RNA export from nucleus / poly(A) binding / poly(U) RNA binding / regulation of alternative mRNA splicing, via spliceosome / positive regulation of translational initiation / signaling adaptor activity / SH2 domain binding ...regulation of RNA export from nucleus / Grb2-Sos complex / PTK6 Regulates Proteins Involved in RNA Processing / positive regulation of RNA export from nucleus / poly(A) binding / poly(U) RNA binding / regulation of alternative mRNA splicing, via spliceosome / positive regulation of translational initiation / signaling adaptor activity / SH2 domain binding / protein tyrosine kinase binding / SH3 domain binding / mRNA processing / G1/S transition of mitotic cell cycle / G2/M transition of mitotic cell cycle / T cell receptor signaling pathway / spermatogenesis / protein domain specific binding / negative regulation of DNA-templated transcription / mRNA binding / protein-containing complex binding / negative regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / RNA binding / nucleoplasm / identical protein binding / membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
Sam68, tyrosine-rich domain / KHDRBS, Qua1 domain / Qua1 domain / Tyrosine-rich domain of Sam68 / KH domain-containing BBP-like / KH domain / K Homology domain, type 1 / Type-1 KH domain profile. / K Homology domain, type 1 superfamily / K Homology domain / K homology RNA-binding domain
Similarity search - Domain/homology
IODIDE ION / KH domain-containing, RNA-binding, signal transduction-associated protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.76 Å
AuthorsNadal, M. / Fuentes-Prior, P.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: Protein Sci. / Year: 2023
Title: Structure and function analysis of Sam68 and hnRNP A1 synergy in the exclusion of exon 7 from SMN2 transcripts.
Authors: Nadal, M. / Anton, R. / Dorca-Arevalo, J. / Estebanez-Perpina, E. / Tizzano, E.F. / Fuentes-Prior, P.
History
DepositionMar 16, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 1, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 12, 2023Group: Database references / Category: citation / Item: _citation.journal_volume / _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
Revision 1.3Oct 9, 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
AAA: Isoform 2 of KH domain-containing, RNA-binding, signal transduction-associated protein 1
BBB: Isoform 2 of KH domain-containing, RNA-binding, signal transduction-associated protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,29821
Polymers26,9522
Non-polymers1,34619
Water37821
1
AAA: Isoform 2 of KH domain-containing, RNA-binding, signal transduction-associated protein 1
hetero molecules

AAA: Isoform 2 of KH domain-containing, RNA-binding, signal transduction-associated protein 1
hetero molecules


  • defined by author
  • Evidence: gel filtration, cross-linking
  • 28.7 kDa, 2 polymers
Theoretical massNumber of molelcules
Total (without water)28,70726
Polymers26,9522
Non-polymers1,75524
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area6870 Å2
ΔGint-22 kcal/mol
Surface area15180 Å2
2
BBB: Isoform 2 of KH domain-containing, RNA-binding, signal transduction-associated protein 1
hetero molecules

BBB: Isoform 2 of KH domain-containing, RNA-binding, signal transduction-associated protein 1
hetero molecules


  • defined by author
  • 27.9 kDa, 2 polymers
Theoretical massNumber of molelcules
Total (without water)27,88916
Polymers26,9522
Non-polymers93714
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area4300 Å2
ΔGint-29 kcal/mol
Surface area14810 Å2
Unit cell
Length a, b, c (Å)97.778, 97.500, 81.919
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number17
Space group name H-MP2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11AAA
21BBB

NCS domain segments:

Ens-ID: 1 / Beg auth comp-ID: ASN / Beg label comp-ID: ASN / End auth comp-ID: ASP / End label comp-ID: ASP / Auth seq-ID: 144 - 261 / Label seq-ID: 1 - 118

Dom-IDComponent-IDAuth asym-IDLabel asym-ID
11AAAA
22BBBB

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

-
Components

#1: Protein Isoform 2 of KH domain-containing, RNA-binding, signal transduction-associated protein 1 / GAP-associated tyrosine phosphoprotein p62 / Src-associated in mitosis 68 kDa protein / Sam68 / p21 ...GAP-associated tyrosine phosphoprotein p62 / Src-associated in mitosis 68 kDa protein / Sam68 / p21 Ras GTPase-activating protein-associated p62 / p68


Mass: 13475.904 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KHDRBS1, SAM68 / Production host: Escherichia coli (E. coli) / References: UniProt: Q07666
#2: Chemical ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: I
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.57 Å3/Da
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 1.8 M ammonium sulfate, 0.1 M sodium iodide

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 7, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 2.76→48.937 Å / Num. obs: 19107 / % possible obs: 94 % / Redundancy: 3.8 % / CC1/2: 0.999 / Net I/σ(I): 14.5
Reflection shellResolution: 2.76→2.86 Å / Num. unique obs: 1894 / CC1/2: 0.483

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5EMO

5emo


Resolution: 2.76→48.937 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.941 / SU B: 9.838 / SU ML: 0.181 / Cross valid method: FREE R-VALUE / ESU R: 0.253 / ESU R Free: 0.225 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.2358 942 4.93 %
Rwork0.1992 18165 -
all0.201 --
obs-19107 91.976 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 92.094 Å2
Baniso -1Baniso -2Baniso -3
1-0.564 Å2-0 Å2-0 Å2
2---5.466 Å20 Å2
3---4.902 Å2
Refinement stepCycle: LAST / Resolution: 2.76→48.937 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1884 0 76 21 1981
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0121981
X-RAY DIFFRACTIONr_angle_refined_deg1.8491.6572624
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1095234
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.96323.33390
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.4915382
X-RAY DIFFRACTIONr_dihedral_angle_4_deg27.855158
X-RAY DIFFRACTIONr_chiral_restr0.1530.2232
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021428
X-RAY DIFFRACTIONr_nbd_refined0.2440.2786
X-RAY DIFFRACTIONr_nbtor_refined0.3170.21268
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.180.252
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2320.269
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.8140.26
X-RAY DIFFRACTIONr_mcbond_it8.7498.643942
X-RAY DIFFRACTIONr_mcangle_it10.80212.9221174
X-RAY DIFFRACTIONr_scbond_it12.4339.5181039
X-RAY DIFFRACTIONr_scangle_it16.25913.851450
X-RAY DIFFRACTIONr_lrange_it17.657163.2417390
X-RAY DIFFRACTIONr_ncsr_local_group_10.0530.053645
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AAAX-RAY DIFFRACTIONLocal ncs0.0530.0501
12BBBX-RAY DIFFRACTIONLocal ncs0.0530.0501
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.76-2.8320.402800.4721275X-RAY DIFFRACTION90.0931
2.832-2.9090.383630.4321338X-RAY DIFFRACTION94.9187
2.909-2.9930.454550.4261287X-RAY DIFFRACTION94.841
2.993-3.0850.404570.381260X-RAY DIFFRACTION94.8847
3.085-3.1870.364620.2941209X-RAY DIFFRACTION93.9394
3.187-3.2980.306590.2451164X-RAY DIFFRACTION93.2876
3.298-3.4230.249490.2211138X-RAY DIFFRACTION93.7599
3.423-3.5620.209440.2081082X-RAY DIFFRACTION92.5226
3.562-3.720.225840.1821003X-RAY DIFFRACTION92.5106
3.72-3.9020.204790.172959X-RAY DIFFRACTION91.6152
3.902-4.1120.195430.162948X-RAY DIFFRACTION92.5303
4.112-4.3610.149390.16874X-RAY DIFFRACTION91.9436
4.361-4.6620.204410.149836X-RAY DIFFRACTION90.8808
4.662-5.0340.21440.149768X-RAY DIFFRACTION91.0314
5.034-5.5130.211200.17733X-RAY DIFFRACTION89.5363
5.513-6.1620.329350.201638X-RAY DIFFRACTION88.5526
6.162-7.110.277210.209572X-RAY DIFFRACTION87.9822
7.11-8.6970.259320.168481X-RAY DIFFRACTION88.4483
8.697-12.2510.162190.156388X-RAY DIFFRACTION86.2288
12.251-48.9370.271160.248212X-RAY DIFFRACTION79.4425

+
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