[English] 日本語
Yorodumi
- PDB-6ne6: Crystal Structure of heterotrimeric G-protein alpha subunit Galph... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ne6
TitleCrystal Structure of heterotrimeric G-protein alpha subunit Galpha7 from Naegleria fowleri
ComponentsG-protein alpha subunit Galpha7
KeywordsCELL CYCLE / SSGCID / guanine nucleotide binding / G protein / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homologyGI Alpha 1, domain 2-like / GI Alpha 1, domain 2-like / Orthogonal Bundle / Mainly Alpha
Function and homology information
Biological speciesNaegleria fowleri (brain-eating amoeba)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To Be Published
Title: Crystal Structure of heterotrimeric G-protein alpha subunit Galpha7 from Naegleria fowleri
Authors: Dranow, D.M. / Abendroth, J. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionDec 17, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: G-protein alpha subunit Galpha7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,87610
Polymers38,3961
Non-polymers4809
Water5,873326
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1570 Å2
ΔGint5 kcal/mol
Surface area16880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.690, 68.310, 79.570
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein G-protein alpha subunit Galpha7


Mass: 38395.633 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Naegleria fowleri (brain-eating amoeba)
Gene: NF0037180 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 326 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.15 Å3/Da / Density % sol: 42.68 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: NafoA.01088.e.B1 and NafoA.19531.b.B2 were co-purified (PW38434) to 20.24 mg/ml in a buffer containing 25 mM HEPES pH 7.5, 500 mM NaCl, 5% Glycerol , 2 mM DTT, 0.025% Azide, 10mM MgCl2, 10mM ...Details: NafoA.01088.e.B1 and NafoA.19531.b.B2 were co-purified (PW38434) to 20.24 mg/ml in a buffer containing 25 mM HEPES pH 7.5, 500 mM NaCl, 5% Glycerol , 2 mM DTT, 0.025% Azide, 10mM MgCl2, 10mM NaF, 30uM AlCl3, 5uM GDP, was mixed 1:1 with Wiz3/4(c8): 16% (w/v) PEG-800, 40 mM potassium phosphate monobasic, 20% (v/v) glycerol, cryoprotected with 20% ethylene glycol. Tray 299259c8, puck: rhn8-4

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Apr 5, 2018 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.7→48.256 Å / Num. obs: 37029 / % possible obs: 99.8 % / Redundancy: 6.003 % / Biso Wilson estimate: 19.7 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.046 / Rrim(I) all: 0.05 / Χ2: 1.039 / Net I/σ(I): 23.09 / Num. measured all: 222267
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.7-1.744.9960.5122.9913464270126950.8580.57299.8
1.74-1.795.90.4194.2215624264826480.9340.459100
1.79-1.846.1570.3315.5115774256225620.9580.361100
1.84-1.96.1650.2517.3815425250325020.9740.274100
1.9-1.966.1210.1869.8314775241424140.9850.203100
1.96-2.036.1710.14812.2114365232923280.990.162100
2.03-2.116.1480.11615.0413894226022600.9940.127100
2.11-2.196.1680.09418.2513490218921870.9950.10399.9
2.19-2.296.1390.07522.3512874209820970.9970.082100
2.29-2.46.1410.06525.0812344201220100.9970.07199.9
2.4-2.536.1520.05827.911751191219100.9980.06399.9
2.53-2.696.1270.0531.7711152182118200.9980.05599.9
2.69-2.876.1010.04236.5510396170517040.9990.04599.9
2.87-3.16.0760.03640.919715160015990.9990.0499.9
3.1-3.46.0820.03146.648923147814670.9990.03499.3
3.4-3.86.0230.02553.228089135213430.9990.02899.3
3.8-4.395.9550.02357.817092119411910.9990.02599.7
4.39-5.385.9260.02258.756033102210180.9990.02499.6
5.38-7.65.7450.02455.7446888218160.9990.02699.4
7.6-48.2565.2380.02258.8823994764580.9990.02596.2

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.24data extraction
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5do9

5do9


Resolution: 1.7→48.256 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 18.73
RfactorNum. reflection% reflectionSelection details
Rfree0.1947 2146 5.99 %0
Rwork0.1609 ---
obs0.163 35817 96.55 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 76.9 Å2 / Biso mean: 24.1924 Å2 / Biso min: 5.23 Å2
Refinement stepCycle: final / Resolution: 1.7→48.256 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2636 0 30 334 3000
Biso mean--41.38 34.74 -
Num. residues----327
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6999-1.73950.2485960.2252033212988
1.7395-1.7830.27821270.20842107223491
1.783-1.83120.24181380.18872133227194
1.8312-1.88510.20651520.17432155230795
1.8851-1.94590.20991490.16072218236797
1.9459-2.01550.18931620.15982209237197
2.0155-2.09620.19491470.16022217236497
2.0962-2.19160.21071290.15712268239798
2.1916-2.30710.17321460.1572262240898
2.3071-2.45170.1841450.15252286243198
2.4517-2.6410.18971530.15862307246099
2.641-2.90670.21211530.15522302245599
2.9067-3.32720.20121490.15872341249099
3.3272-4.19160.16121450.14512367251299
4.1916-48.27510.20031550.16862466262199
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)
11.1439-0.7207-0.2271.6130.36261.4431-0.03630.2402-0.0247-0.06470.01040.10650.0518-0.02690.0240.1151-0.01130.00120.130.02040.12140.138738.3353-3.812
21.93663.01253.71124.69645.79627.1347-0.09280.08060.1061-0.1280.01190.0276-0.2410.15840.0680.13450.02330.020.14750.02960.147823.575839.32628.4888
31.1835-0.38761.20351.4549-1.20113.0056-0.01560.10550.12320.0154-0.2771-0.31010.04030.47370.17150.1523-0.01420.0020.21230.0290.23634.065441.928117.5709
41.2315-0.07610.51771.6254-0.08631.66620.0138-0.0206-0.07250.0263-0.03-0.0140.10440.1244-0.00780.11780.0072-0.00690.13110.02680.12924.306336.046815.7465
53.5932-0.24061.88260.532-0.09861.74890.02420.1226-0.0884-0.0171-0.02420.05490.06250.03410.01890.1623-0.01040.01290.15250.0060.14676.585635.3267-0.7778
61.94210.48081.01261.12671.24221.6095-0.1630.487-0.0515-0.25670.1103-0.0122-0.30010.40150.04270.2232-0.01950.00770.24630.03560.20634.111649.1482.302
71.1857-0.13890.87861.8375-0.67492.379-0.0237-0.07510.02870.14020.00510.1209-0.1359-0.12520.02070.10190.01580.02720.09930.00050.1272-2.635148.958716.6186
89.4354-8.58885.56648.8982-4.65754.58180.1197-0.13210.0497-0.022-0.03110.18810.1003-0.2289-0.11040.1428-0.03570.03940.14420.01970.2368-11.99538.24883.6828
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 27 through 62 )A27 - 62
2X-RAY DIFFRACTION2chain 'A' and (resid 63 through 90 )A63 - 90
3X-RAY DIFFRACTION3chain 'A' and (resid 91 through 116 )A91 - 116
4X-RAY DIFFRACTION4chain 'A' and (resid 117 through 165 )A117 - 165
5X-RAY DIFFRACTION5chain 'A' and (resid 166 through 203 )A166 - 203
6X-RAY DIFFRACTION6chain 'A' and (resid 204 through 244 )A204 - 244
7X-RAY DIFFRACTION7chain 'A' and (resid 245 through 331 )A245 - 331
8X-RAY DIFFRACTION8chain 'A' and (resid 332 through 353 )A332 - 353

+
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