[English] 日本語
Yorodumi
- PDB-8sjj: X-ray structure of the metastable SEPT14-SEPT7 heterodimeric coil... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8sjj
TitleX-ray structure of the metastable SEPT14-SEPT7 heterodimeric coiled coil
Components
  • Septin 7
  • Septin-14
KeywordsCELL CYCLE / Septin / Coiled coil
Function / homology
Function and homology information


septin complex / protein localization to perinuclear region of cytoplasm / septin ring / cytoskeleton-dependent cytokinesis / motile cilium / cell division site / cilium assembly / spermatid development / acrosomal vesicle / kinetochore ...septin complex / protein localization to perinuclear region of cytoplasm / septin ring / cytoskeleton-dependent cytokinesis / motile cilium / cell division site / cilium assembly / spermatid development / acrosomal vesicle / kinetochore / neuron migration / intracellular protein localization / microtubule cytoskeleton / spermatogenesis / perikaryon / molecular adaptor activity / cytoskeleton / axon / GTPase activity / dendrite / GTP binding / perinuclear region of cytoplasm / cytoplasm
Similarity search - Function
Septin 7 / Septin-type guanine nucleotide-binding (G) domain / Septin / Septin-type guanine nucleotide-binding (G) domain profile. / Septin / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Septin / Septin-14
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.781 Å
AuthorsCavini, I.A. / Pereira, H.M. / Garratt, R.C.
Funding support Brazil, 2items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)20/02897-1 Brazil
Sao Paulo Research Foundation (FAPESP)18/19992-7 Brazil
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2023
Title: X-ray structure of the metastable SEPT14-SEPT7 coiled coil reveals a hendecad region crucial for heterodimerization.
Authors: Cavini, I.A. / Winter, A.J. / D'Muniz Pereira, H. / Woolfson, D.N. / Crump, M.P. / Garratt, R.C.
History
DepositionApr 18, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 27, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Septin-14
B: Septin-14
C: Septin 7
D: Septin 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,76614
Polymers40,3704
Non-polymers39610
Water4,450247
1
A: Septin-14
C: Septin 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,3837
Polymers20,1852
Non-polymers1985
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Septin-14
hetero molecules

D: Septin 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,3837
Polymers20,1852
Non-polymers1985
Water362
TypeNameSymmetry operationNumber
crystal symmetry operation2_455-x-1,y+1/2,-z1
crystal symmetry operation2_355-x-2,y+1/2,-z1
Unit cell
Length a, b, c (Å)34.934, 50.811, 91.558
Angle α, β, γ (deg.)90.00, 94.36, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Septin-14


Mass: 9249.529 Da / Num. of mol.: 2 / Fragment: coiled coil domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SEPTIN14, SEPT14 / Plasmid: pETSUMO / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: Q6ZU15
#2: Protein Septin 7


Mass: 10935.504 Da / Num. of mol.: 2 / Fragment: residues 307-390
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pETSUMO / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: A0A023T695
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 247 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.01 Å3/Da / Density % sol: 38.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 0.1 M Bis-Tris pH 5.0, 24% PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Feb 25, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.781→91.294 Å / Num. obs: 22355 / % possible obs: 72.47 % / Redundancy: 6.83 % / CC1/2: 0.999 / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.041 / Rrim(I) all: 0.108 / Net I/σ(I): 10.602
Reflection shellResolution: 1.781→1.996 Å / Rmerge(I) obs: 1.168 / Mean I/σ(I) obs: 1.29 / Num. unique obs: 1118 / CC1/2: 0.5692 / Rpim(I) all: 0.535 / Rrim(I) all: 1.1289 / % possible all: 14.18

-
Processing

Software
NameVersionClassification
BUSTER2.10.3 (6-FEB-2020)refinement
STARANISOdata scaling
autoPROCdata reduction
Arcimboldophasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.781→91.29 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.881 / SU R Cruickshank DPI: 0.228 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.241 / SU Rfree Blow DPI: 0.208 / SU Rfree Cruickshank DPI: 0.204
RfactorNum. reflection% reflectionSelection details
Rfree0.2863 1141 5.1 %RANDOM
Rwork0.2206 ---
obs0.2238 22355 72.5 %-
Displacement parametersBiso mean: 32.76 Å2
Baniso -1Baniso -2Baniso -3
1--2.4664 Å20 Å22.1453 Å2
2--0.155 Å20 Å2
3---2.3114 Å2
Refine analyzeLuzzati coordinate error obs: 0.31 Å
Refinement stepCycle: LAST / Resolution: 1.781→91.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2609 0 22 247 2878
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0082705HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.853590HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1090SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes479HARMONIC5
X-RAY DIFFRACTIONt_it2705HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.33
X-RAY DIFFRACTIONt_other_torsion18.43
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion335SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2669SEMIHARMONIC4
LS refinement shellResolution: 1.781→1.9 Å
RfactorNum. reflection% reflection
Rfree0.2485 -5.58 %
Rwork0.2148 423 -
obs--8.14 %
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)
10.60010.82881.26960.3550.9221.6076-0.1558-0.08850.0529-0.1881-0.0010.0184-0.4099-0.20780.1568-0.10150.0352-0.02460.0698-0.1208-0.03264.972540.379922.1596
22.4381.41912.19980.85421.27721.8914-0.33360.27510.1479-0.21410.17810.0792-0.4350.27030.1555-0.04890.0062-0.0314-0.0568-0.0267-0.04183.232514.3820.3236
31.14440.97541.85181.07511.80513.38910.01150.01960.09430.0702-0.14430.15840.2002-0.0030.1328-0.06880.0092-0.0531-0.025-0.0515-0.03976.197930.485618.7291
40.95370.50210.95460.18220.2880.72320.09470.363-0.30890.03060.2548-0.18090.05840.5014-0.3495-0.07970.0415-0.0448-0.0224-0.0944-0.0091-28.56675.587721.3029
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }

+
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