[English] 日本語
Yorodumi
- PDB-6upq: Crystal Structure of GTPase Domain of Human Septin 2 / Septin 11 ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6upq
TitleCrystal Structure of GTPase Domain of Human Septin 2 / Septin 11 Heterocomplex
Components
  • Septin-11
  • Septin-2
KeywordsSTRUCTURAL PROTEIN / cytoskeleton protein / septin
Function / homology
Function and homology information


postsynaptic specialization of symmetric synapse / sperm annulus / septin complex / photoreceptor connecting cilium / septin ring / cytoskeleton-dependent cytokinesis / regulation of exocytosis / non-motile cilium / ciliary membrane / smoothened signaling pathway ...postsynaptic specialization of symmetric synapse / sperm annulus / septin complex / photoreceptor connecting cilium / septin ring / cytoskeleton-dependent cytokinesis / regulation of exocytosis / non-motile cilium / ciliary membrane / smoothened signaling pathway / intercellular bridge / cell division site / regulation of synapse organization / cleavage furrow / axoneme / cilium assembly / stress fiber / GABA-ergic synapse / Anchoring of the basal body to the plasma membrane / kinetochore / spindle / microtubule cytoskeleton / protein localization / actin cytoskeleton / synaptic vesicle / midbody / spermatogenesis / molecular adaptor activity / dendritic spine / cell differentiation / cadherin binding / axon / GTPase activity / glutamatergic synapse / GTP binding / extracellular exosome / nucleoplasm / identical protein binding / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Septin 2 / 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
GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / Septin-2 / Septin-11
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.86 Å
AuthorsLeonardo, D.A. / Pereira, H.M. / Brandao-Neto, J. / Araujo, A.P.U. / Garratt, R.C.
Funding support Brazil, 2items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2014/15546-1 Brazil
Sao Paulo Research Foundation (FAPESP)2016/04658-9 Brazil
CitationJournal: J.Mol.Biol. / Year: 2020
Title: Molecular Recognition at Septin Interfaces: The Switches Hold the Key.
Authors: Rosa, H.V.D. / Leonardo, D.A. / Brognara, G. / Brandao-Neto, J. / D'Muniz Pereira, H. / Araujo, A.P.U. / Garratt, R.C.
History
DepositionOct 18, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 30, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 28, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 11, 2023Group: 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: Septin-2
B: Septin-11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,3315
Polymers65,3412
Non-polymers9913
Water8,971498
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering, gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5880 Å2
ΔGint-31 kcal/mol
Surface area23420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.654, 81.859, 68.221
Angle α, β, γ (deg.)90.000, 97.130, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 2 types, 2 molecules AB

#1: Protein Septin-2 / Neural precursor cell expressed developmentally down-regulated protein 5 / NEDD-5


Mass: 31691.299 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SEPTIN2, DIFF6, KIAA0158, NEDD5, SEPT2 / Plasmid: pET-Duet-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: Q15019
#2: Protein Septin-11


Mass: 33649.387 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SEPTIN11, SEPT11 / Plasmid: pET-Duet-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: Q9NVA2

-
Non-polymers , 4 types, 501 molecules

#3: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM
#4: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: GTP, energy-carrying molecule*YM
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 498 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 48.8 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 100mM MES/imidazole pH 6.5, 10% PEG 20000, 20% PEG 550 MME and 30mM of each sodium nitrate, disodium hydrogen phosphate and ammonium sulfate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96863 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96863 Å / Relative weight: 1
ReflectionResolution: 1.86→67.7 Å / Num. obs: 51728 / % possible obs: 99.6 % / Redundancy: 6.7 % / CC1/2: 0.973 / Rmerge(I) obs: 0.192 / Rpim(I) all: 0.08 / Rrim(I) all: 0.208 / Net I/σ(I): 5.8 / Num. measured all: 347126 / Scaling rejects: 910
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.86-1.916.83.1262567637980.4531.2923.3870.998.9
8.32-67.76.40.0639146110.9960.0260.06515.599.9

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
Aimless0.7.2data scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
xia2data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6UPA

6upa


Resolution: 1.86→56.216 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 24.59
RfactorNum. reflection% reflectionSelection details
Rfree0.2178 2567 4.97 %Random selection
Rwork0.1867 ---
obs0.1882 51621 99.31 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 124.71 Å2 / Biso mean: 37.0276 Å2 / Biso min: 15.17 Å2
Refinement stepCycle: final / Resolution: 1.86→56.216 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4130 0 61 498 4689
Biso mean--21.2 41.32 -
Num. residues----517
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.86-1.89570.39171430.3696268798
1.8957-1.93440.39811610.3687264298
1.9344-1.97640.33251560.2835268799
1.9764-2.02240.30181340.2581272899
2.0224-2.0730.29151350.2376271699
2.073-2.1290.2631370.2312271099
2.129-2.19170.24231390.2131270899
2.1917-2.26240.29811390.2618272799
2.2624-2.34330.23961350.2007268499
2.3433-2.43710.22471440.197274099
2.4371-2.5480.251460.18442729100
2.548-2.68240.20381370.18272724100
2.6824-2.85040.21261330.17872764100
2.8504-3.07050.20091380.17512724100
3.0705-3.37950.19021350.16462753100
3.3795-3.86840.19261660.15452746100
3.8684-4.87330.1751290.14092785100
4.8733-56.2160.17031600.1612800100
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)
17.72013.06760.77435.35253.52582.8564-0.09360.15690.2093-0.22420.10920.0851-0.2163-0.16320.01860.14160.02470.01910.15420.0010.14537.15739.8846.9492
24.0408-0.89732.6552.096-0.57584.8431-0.1264-0.36460.22950.10910.034-0.081-0.4515-0.6218-0.02950.28060.10060.01370.4257-0.04110.31433.279712.152919.5096
35.5579-0.27891.61815.8366-1.56947.27640.08451.04690.6879-0.6104-0.1850.2122-1.15820.12490.09770.48190.0742-0.02150.5280.09750.4177-0.36414.7634-0.1286
40.27210.2702-0.0730.4915-0.7221.73150.2986-0.8087-0.15690.0171-0.09780.05390.5722-0.9776-0.19780.3408-0.0697-0.03760.39180.05270.30123.9681-0.526321.2737
56.18921.30861.51881.77821.06622.4086-0.22470.22380.4073-0.26390.00840.5207-0.3369-0.71110.12030.2730.0376-0.07650.386-0.01440.3595-11.71210.91291.826
64.37251.30660.75860.9421-0.07891.41360.09110.0491-0.2213-0.0919-0.0168-0.01890.171-0.012-0.10410.20080.01790.00580.1834-0.03960.192712.2656-1.04299.4198
79.03487.45791.07578.70631.51993.7476-0.04820.5989-1.1049-0.24170.1732-0.84080.35130.3893-0.06840.25360.1186-0.00090.2688-0.07290.30523.1827-5.04126.2482
83.24170.52811.07212.1681.80311.63310.01240.9196-0.1537-1.2878-0.2054-0.18820.63630.35960.13350.54010.07040.03580.4695-0.07690.302511.1904-5.4291-7.2257
92.16480.51350.76772.9480.71921.9009-0.01420.6512-0.2071-0.7538-0.0648-0.0487-0.12590.1929-0.0010.33790.04550.02710.4675-0.03290.212218.3665.5254-4.9757
101.4646-1.5711.71782.0304-0.49047.1901-0.08250.83650.8548-0.9193-0.1749-0.7591-0.52250.68630.01720.4406-0.06480.02010.36890.14030.477324.196223.38094.6454
115.21563.30141.90233.46941.1891.512-0.20550.5370.0057-0.26520.23650.1433-0.06080.0513-0.0120.20210.0310.01170.2464-0.00260.18057.7143.5911-1.7007
124.9071.96821.45872.76981.05773.81260.10660.2793-0.2670.10840.1042-0.3560.33890.5696-0.24740.20690.0802-0.0170.23110.01470.23933.3076-1.690927.9244
133.2316-1.25671.83512.5359-0.04884.78750.12710.2311-0.11390.1665-0.0363-0.29540.29420.5146-0.07320.26660.0125-0.01460.23840.05240.261627.5165-5.982430.8072
140.4599-0.51241.16941.7378-2.78945.351-0.0161-0.0409-0.03130.1078-0.037-0.106-0.0543-0.00670.02280.22460.0137-0.02110.1897-0.01570.217525.6363-0.773839.3667
156.4660.6501-3.76684.4383-2.38963.8129-0.0587-0.050.54460.07150.23860.1724-0.6588-0.5806-0.3320.30160.0788-0.05690.2313-0.03740.277118.818318.099327.0725
162.59060.378-2.68761.2944-0.71485.21280.0025-0.15130.17980.1746-0.0291-0.2429-0.12720.197-0.07040.2050.0171-0.0450.2108-0.00640.250633.773711.17224.0711
170.57410.7181-1.21322.1064-3.83188.59380.0855-0.1717-0.00690.5116-0.2883-0.2746-0.82590.62990.15440.27680.0217-0.03910.2508-0.00830.267133.2788.556235.6691
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 36 through 58 )A36 - 58
2X-RAY DIFFRACTION2chain 'A' and (resid 59 through 81 )A59 - 81
3X-RAY DIFFRACTION3chain 'A' and (resid 82 through 101 )A82 - 101
4X-RAY DIFFRACTION4chain 'A' and (resid 102 through 115 )A102 - 115
5X-RAY DIFFRACTION5chain 'A' and (resid 116 through 147 )A116 - 147
6X-RAY DIFFRACTION6chain 'A' and (resid 148 through 188 )A148 - 188
7X-RAY DIFFRACTION7chain 'A' and (resid 189 through 205 )A189 - 205
8X-RAY DIFFRACTION8chain 'A' and (resid 206 through 221 )A206 - 221
9X-RAY DIFFRACTION9chain 'A' and (resid 222 through 244 )A222 - 244
10X-RAY DIFFRACTION10chain 'A' and (resid 245 through 258 )A245 - 258
11X-RAY DIFFRACTION11chain 'A' and (resid 259 through 305 )A259 - 305
12X-RAY DIFFRACTION12chain 'B' and (resid 40 through 72 )B40 - 72
13X-RAY DIFFRACTION13chain 'B' and (resid 73 through 114 )B73 - 114
14X-RAY DIFFRACTION14chain 'B' and (resid 115 through 189 )B115 - 189
15X-RAY DIFFRACTION15chain 'B' and (resid 190 through 206 )B190 - 206
16X-RAY DIFFRACTION16chain 'B' and (resid 207 through 255 )B207 - 255
17X-RAY DIFFRACTION17chain 'B' and (resid 256 through 300 )B256 - 300

+
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