[English] 日本語
Yorodumi
- PDB-2qag: Crystal structure of human septin trimer 2/6/7 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2qag
TitleCrystal structure of human septin trimer 2/6/7
Components
  • Septin-2
  • Septin-6
  • Septin-7
KeywordsCELL CYCLE / STRUCTURAL PROTEIN / Cell division / GTP-binding / Nucleotide-binding / Phosphorylation / Acetylation / Alternative splicing / Coiled coil
Function / homology
Function and homology information


septin collar / regulation of embryonic cell shape / sperm annulus / septin complex / positive regulation of non-motile cilium assembly / photoreceptor connecting cilium / cytoskeleton-dependent cytokinesis / septin ring / regulation of exocytosis / non-motile cilium ...septin collar / regulation of embryonic cell shape / sperm annulus / septin complex / positive regulation of non-motile cilium assembly / photoreceptor connecting cilium / cytoskeleton-dependent cytokinesis / septin ring / regulation of exocytosis / non-motile cilium / ciliary membrane / smoothened signaling pathway / cell division site / intercellular bridge / axoneme / cleavage furrow / mitotic cytokinesis / cilium assembly / axon terminus / stress fiber / Anchoring of the basal body to the plasma membrane / MAPK6/MAPK4 signaling / spindle / kinetochore / microtubule cytoskeleton / synaptic vesicle / actin cytoskeleton / midbody / spermatogenesis / cell differentiation / molecular adaptor activity / cadherin binding / GTPase activity / GTP binding / structural molecule activity / extracellular exosome / nucleoplasm / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Septin 2 / Septin 7 / Septin-type guanine nucleotide-binding (G) domain / Septin / Septin-type guanine nucleotide-binding (G) domain profile. / Septin / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / Septin-6 / Septin-2 / Septin-7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 4 Å
AuthorsSirajuddin, M.
CitationJournal: Nature / Year: 2007
Title: Structural insight into filament formation by mammalian septins.
Authors: Sirajuddin, M. / Farkasovsky, M. / Hauer, F. / Kuhlmann, D. / Macara, I.G. / Weyand, M. / Stark, H. / Wittinghofer, A.
History
DepositionJun 15, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Septin-2
B: Septin-6
C: Septin-7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,7476
Polymers139,3373
Non-polymers1,4103
Water0
1
A: Septin-2
B: Septin-6
C: Septin-7
hetero molecules

A: Septin-2
B: Septin-6
C: Septin-7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)281,49412
Polymers278,6746
Non-polymers2,8196
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_655-x+1,y,-z1
Unit cell
Length a, b, c (Å)252.515, 252.515, 156.485
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322
DetailsThe biological assembly is a hexamer, but hexamer is divided by crystallographic symmetry, trimer occupies the asymmetric unit. Trimer model was generated from Sept2 (2QA5, submitted recently).

-
Components

#1: Protein Septin-2 / / Protein NEDD5


Mass: 41550.508 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SEPT2, DIFF6, KIAA0158, NEDD5 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta BL21 / References: UniProt: Q15019
#2: Protein Septin-6 /


Mass: 48948.723 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SEPT6, KIAA0128, SEP2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q14141
#3: Protein Septin-7 / / CDC10 protein homolog


Mass: 48837.945 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SEPT7, CDC10 / Production host: Escherichia coli (E. coli) / References: UniProt: Q16181
#4: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#5: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine triphosphate


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 8.95 Å3/Da / Density % sol: 86.26 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.4M Ammonium Sulfate, 0.1M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.07188 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 21, 2006
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07188 Å / Relative weight: 1
ReflectionResolution: 4→50 Å / Num. obs: 42485 / Redundancy: 16.2 % / Rsym value: 0.229 / Net I/σ(I): 11.42
Reflection shellResolution: 4→4.1 Å / Rmerge(I) obs: 0.379 / Mean I/σ(I) obs: 3.98 / % possible all: 98.9

-
Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
PDB_EXTRACT2data extraction
SOLVEphasing
RefinementMethod to determine structure: MIRAS / Resolution: 4→49.15 Å / Cor.coef. Fo:Fc: 0.796 / Cor.coef. Fo:Fc free: 0.787 / SU B: 82.738 / SU ML: 0.616 / Cross valid method: THROUGHOUT / ESU R: 0.7 / ESU R Free: 0.54
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Sept6 (Chain B) and Sept7 (Chain C) will have poly-alanine stretches due low resolution.
RfactorNum. reflection% reflectionSelection details
Rfree0.39208 2125 5 %RANDOM
Rwork0.37554 ---
obs0.37637 40358 98.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 78.174 Å2
Baniso -1Baniso -2Baniso -3
1--14.93 Å20 Å20 Å2
2---14.93 Å20 Å2
3---29.85 Å2
Refinement stepCycle: LAST / Resolution: 4→49.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4407 0 88 0 4495
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0570.0224612
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg4.7191.9546311
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg18.8755681
X-RAY DIFFRACTIONr_dihedral_angle_2_deg51.52425.25897
X-RAY DIFFRACTIONr_dihedral_angle_3_deg30.80315461
X-RAY DIFFRACTIONr_dihedral_angle_4_deg5.216156
X-RAY DIFFRACTIONr_chiral_restr0.2470.2808
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.023366
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.4750.23293
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3750.22772
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.4030.2320
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3390.215
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7471.53815
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.84425299
X-RAY DIFFRACTIONr_scbond_it3.27631223
X-RAY DIFFRACTIONr_scangle_it5.1234.51012
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 4→4.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.454 156 -
Rwork0.467 2948 -
obs--98.95 %

+
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