[English] 日本語
Yorodumi
- PDB-6rup: Human mitochondrial single-stranded DNA binding protein, SSBP1, a... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6rup
TitleHuman mitochondrial single-stranded DNA binding protein, SSBP1, at 2.1 A resolution - elucidated sequence
Components
  • SER-SER-SER-SER
  • Single-stranded DNA-binding protein, mitochondrial
KeywordsDNA BINDING PROTEIN / Single-stranded DNA binding protein / mitochondria / mtDNA / mtDNA replication / mitochondrial RNA granules
Function / homology
Function and homology information


positive regulation of mitochondrial DNA replication / positive regulation of helicase activity / mitochondrial DNA replication / DNA unwinding involved in DNA replication / mitochondrial nucleoid / Transcriptional activation of mitochondrial biogenesis / single-stranded DNA binding / protein homotetramerization / mitochondrial matrix / chromatin binding ...positive regulation of mitochondrial DNA replication / positive regulation of helicase activity / mitochondrial DNA replication / DNA unwinding involved in DNA replication / mitochondrial nucleoid / Transcriptional activation of mitochondrial biogenesis / single-stranded DNA binding / protein homotetramerization / mitochondrial matrix / chromatin binding / protein homodimerization activity / mitochondrion / RNA binding / extracellular exosome / identical protein binding / nucleus
Similarity search - Function
Single-stranded DNA-binding protein / Single-strand binding protein family / Single-strand binding (SSB) domain profile. / Primosome PriB/single-strand DNA-binding / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Single-stranded DNA-binding protein, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsTarres-Sole, A. / Chakraborty, A. / Spelbrink, H.N. / Delettre, C. / Sola, M.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and Universities Spain
Citation
Journal: J.Clin.Invest. / Year: 2020
Title: Dominant mutations in mtDNA maintenance gene SSBP1 cause optic atrophy and foveopathy.
Authors: Piro-Megy, C. / Sarzi, E. / Tarres-Sole, A. / Pequignot, M. / Hensen, F. / Quiles, M. / Manes, G. / Chakraborty, A. / Senechal, A. / Bocquet, B. / Cazevieille, C. / Roubertie, A. / Muller, A. ...Authors: Piro-Megy, C. / Sarzi, E. / Tarres-Sole, A. / Pequignot, M. / Hensen, F. / Quiles, M. / Manes, G. / Chakraborty, A. / Senechal, A. / Bocquet, B. / Cazevieille, C. / Roubertie, A. / Muller, A. / Charif, M. / Goudenege, D. / Lenaers, G. / Wilhelm, H. / Kellner, U. / Weisschuh, N. / Wissinger, B. / Zanlonghi, X. / Hamel, C. / Spelbrink, J.N. / Sola, M. / Delettre, C.
#1: Journal: Nucleic Acids Res. / Year: 2019
Title: Mitochondrial RNA granules are critically dependent on mtDNA replication factors Twinkle and mtSSB.
Authors: Hensen, F. / Potter, A. / van Esveld, S.L. / Tarres-Sole, A. / Chakraborty, A. / Sola, M. / Spelbrink, J.N.
History
DepositionMay 28, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 9, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Single-stranded DNA-binding protein, mitochondrial
B: Single-stranded DNA-binding protein, mitochondrial
C: SER-SER-SER-SER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,3945
Polymers33,3453
Non-polymers492
Water1,71195
1
A: Single-stranded DNA-binding protein, mitochondrial
B: Single-stranded DNA-binding protein, mitochondrial
C: SER-SER-SER-SER
hetero molecules

A: Single-stranded DNA-binding protein, mitochondrial
B: Single-stranded DNA-binding protein, mitochondrial
C: SER-SER-SER-SER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,78810
Polymers66,6916
Non-polymers974
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Unit cell
Length a, b, c (Å)51.040, 51.040, 182.340
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11B-202-

MG

-
Components

#1: Protein Single-stranded DNA-binding protein, mitochondrial / MtSSB / PWP1-interacting protein 17


Mass: 16489.557 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SSBP1, SSBP / Plasmid: pCRI7a / Production host: Escherichia coli (E. coli) / Variant (production host): codon+ / References: UniProt: Q04837
#2: Protein/peptide SER-SER-SER-SER


Mass: 366.326 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 95 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

Crystal growTemperature: 293 K / Method: evaporation / pH: 6.5
Details: 11 % PEG1500, 0.1 M cacodylate pH 6.5, 0.2 M magnesium chloride. cryoprotectant solution included

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 R CdTe 300K / Detector: PIXEL / Date: Oct 28, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.1→45.58 Å / Num. obs: 14943 / % possible obs: 99.5 % / Observed criterion σ(I): 1.09 / Redundancy: 11 % / Biso Wilson estimate: 52.63 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.096 / Net I/σ(I): 16.28
Reflection shellResolution: 2.1→2.23 Å / Redundancy: 11.2 % / Num. unique obs: 2342 / CC1/2: 0.542 / Rrim(I) all: 0.245 / % possible all: 97.5

-
Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ULL

3ull


Resolution: 2.1→45.58 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.935 / SU R Cruickshank DPI: 0.21 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.228 / SU Rfree Blow DPI: 0.19 / SU Rfree Cruickshank DPI: 0.185
RfactorNum. reflection% reflectionSelection details
Rfree0.249 776 5.22 %RANDOM
Rwork0.2 ---
obs0.202 14874 99.6 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.0427 Å20 Å20 Å2
2---2.0427 Å20 Å2
3---4.0853 Å2
Refine analyzeLuzzati coordinate error obs: 0.28 Å
Refinement stepCycle: 1 / Resolution: 2.1→45.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1764 0 2 95 1861
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0081791HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.982417HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d842SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes39HARMONIC2
X-RAY DIFFRACTIONt_gen_planes261HARMONIC5
X-RAY DIFFRACTIONt_it1791HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion6.83
X-RAY DIFFRACTIONt_other_torsion2.87
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion235SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance1HARMONIC1
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2100SEMIHARMONIC4
LS refinement shellResolution: 2.1→2.27 Å / Rfactor Rfree error: 0 / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.254 174 5.94 %
Rwork0.219 2753 -
all0.221 2927 -
obs--97.99 %
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)
12.29190.5408-0.15492.77780.80022.21890.04560.0453-0.2441-0.2415-0.0355-0.10450.2714-0.1048-0.0102-0.06840.00620.0056-0.26230.0163-0.259822.146220.362432.628
20.27660.1239-0.77641.17840.81320.14940.00480.0803-0.05140.0039-0.0197-0.05920.02810.12330.01480.20050.11510.1520.0184-0.10910.270432.648513.947420.67
31.70582.0984-0.05844.514-1.18082.4121-0.0080.01980.06640.09130.05240.11980.032-0.1219-0.04440.30050.1520.0718-0.04640.152-0.03182.093237.956534.2432
400.7652-2.22550.57850.02480.3765-0.00610.06130.0730.0760.0074-0.126-0.1150.0921-0.00130.30060.0980.1520.29930.152-0.293133.262332.531616.0411
500.01140.11290.039-0.08480.005-0.0015-0.0172-0.0090.00650.0009-0.0164-0.00740.00510.00060.1368-0.1484-0.0261-0.15180.04220.116310.151812.364938.1696
61.7818-0.03270.69432.7050.77852.0257-0.0349-0.0680.2568-0.3336-0.0802-0.2645-0.54070.11210.1151-0.0385-0.01680.0131-0.29130.013-0.26825.293941.63535.6207
70-0.04732.4632.35682.83660.02020.0242-0.02480.04180.11910.0588-0.0471-0.02310.0136-0.0830.0750.0598-0.1520.1336-0.09620.0463-0.844927.621431.457
80.6514-0.95941.71251.10740.332500.00410.01810.00810.0101-0.0511-0.0573-0.0308-0.06780.04690.3040.1199-0.1520.10850.1082-0.30412.991449.557326.3304
90.70582.05910.83242.2463-0.33722.3347-0.0253-0.0719-0.1618-0.07160.1713-0.52030.19790.4518-0.14610.21390.00580.0488-0.016-0.08560.109326.209830.956132.0869
100-1.1704-0.06230.97570.8541.5183-0.00870.1978-0.1928-0.0638-0.01150.02770.03410.06160.02020.27650.1520.07780.27080.125-0.249120.770536.566712.0461
1100.413-0.171900.0960-0.0037-0.00350.00560.02720.0077-0.0178-0.00830.0355-0.0041-0.0241-0.1303-0.08580.0236-0.02150.142634.534544.033647.2084
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|25 - A|45 A|54 - A|62 A|81 - A|117 A|129 - A|140}
2X-RAY DIFFRACTION2{ A|46 - A|53 }
3X-RAY DIFFRACTION3{ A|63 - A|80 }
4X-RAY DIFFRACTION4{ A|118 - A|128 }
5X-RAY DIFFRACTION5{ A|141 }
6X-RAY DIFFRACTION6{ B|28 - B|47 B|53 - B|62 B|83 - B|119 B|127 - B|139}
7X-RAY DIFFRACTION7{ B|19 - B|27 }
8X-RAY DIFFRACTION8{ B|48 - B|52 }
9X-RAY DIFFRACTION9{ B|63 - B|82 C|1 - C|4 }
10X-RAY DIFFRACTION10{ B|120 - B|126 }
11X-RAY DIFFRACTION11{ B|140 - B|141 }

+
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