[English] 日本語
Yorodumi
- PDB-4gx2: GsuK channel bound to NAD -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4gx2
TitleGsuK channel bound to NAD
ComponentsTrkA domain protein
KeywordsTRANSPORT PROTEIN / Membrane Protein / Ion Channel / ADP binding / NAD binding / Membrane
Function / homology
Function and homology information


monoatomic cation transmembrane transporter activity / potassium ion transport / nucleotide binding / membrane / metal ion binding
Similarity search - Function
Regulator of K+ conductance, C-terminal domain / : / Regulator of K+ conductance, N-terminal / TrkA-N domain / Regulator of K+ conductance, C-terminal / Regulator of K+ conductance, C-terminal domain superfamily / TrkA-C domain / RCK C-terminal domain profile. / RCK N-terminal domain profile. / Helix Hairpins - #70 ...Regulator of K+ conductance, C-terminal domain / : / Regulator of K+ conductance, N-terminal / TrkA-N domain / Regulator of K+ conductance, C-terminal / Regulator of K+ conductance, C-terminal domain superfamily / TrkA-C domain / RCK C-terminal domain profile. / RCK N-terminal domain profile. / Helix Hairpins - #70 / Potassium channel domain / Ion channel / Helix Hairpins / NAD(P)-binding Rossmann-like Domain / Alpha-Beta Plaits / NAD(P)-binding domain superfamily / Rossmann fold / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / PHOSPHATE ION / TrkA domain protein
Similarity search - Component
Biological speciesGeobacter sulfurreducens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsKong, C. / Zeng, W. / Ye, S. / Chen, L. / Sauer, D.B. / Lam, Y. / Derebe, M.G. / Jiang, Y.
CitationJournal: elife / Year: 2012
Title: Distinct gating mechanisms revealed by the structures of a multi-ligand gated K(+) channel.
Authors: Kong, C. / Zeng, W. / Ye, S. / Chen, L. / Sauer, D.B. / Lam, Y. / Derebe, M.G. / Jiang, Y.
History
DepositionSep 3, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 26, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _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: TrkA domain protein
B: TrkA domain protein
C: TrkA domain protein
D: TrkA domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)251,06430
Polymers247,3294
Non-polymers3,73526
Water90150
1
A: TrkA domain protein
B: TrkA domain protein
hetero molecules

A: TrkA domain protein
B: TrkA domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)251,06430
Polymers247,3294
Non-polymers3,73526
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area13560 Å2
ΔGint-110 kcal/mol
Surface area82050 Å2
MethodPISA
2
C: TrkA domain protein
D: TrkA domain protein
hetero molecules

C: TrkA domain protein
D: TrkA domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)251,06430
Polymers247,3294
Non-polymers3,73526
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_557-x,y,-z+21
Buried area13180 Å2
ΔGint-113 kcal/mol
Surface area82060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)232.548, 111.104, 164.561
Angle α, β, γ (deg.)90.00, 134.78, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-601-

K

21A-602-

K

31A-603-

K

41A-604-

K

51A-605-

K

61B-601-

K

71C-601-

K

81C-602-

K

91C-603-

K

101C-604-

K

111C-605-

K

121D-601-

K

-
Components

-
Protein , 1 types, 4 molecules ABCD

#1: Protein
TrkA domain protein


Mass: 61832.238 Da / Num. of mol.: 4 / Mutation: E52A, Q77E, L97D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacter sulfurreducens (bacteria) / Strain: ATCC 51573 / DSM 12127 / PCA / Gene: GSU0527 / Plasmid: pQE-70 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q74FS9

-
Non-polymers , 6 types, 76 molecules

#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: K
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#5: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#6: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / 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: 3.05 Å3/Da / Density % sol: 59.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 13-18% PEG 3350, 250-500mM KSCN, 100mM CHES, pH 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 78 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97921 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 12, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97921 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 47223 / % possible obs: 95.6 % / Observed criterion σ(I): 1.1727
Reflection shellResolution: 3.2→3.26 Å / % possible all: 92.5

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→41.14 Å / SU ML: 0.43 / σ(F): 1.34 / Phase error: 29.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2702 2382 5.06 %Random
Rwork0.23 ---
obs0.2321 47062 95.51 %-
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.479 Å2 / ksol: 0.261 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-11.7551 Å2-0 Å2-0.0396 Å2
2---29.551 Å20 Å2
3---17.7959 Å2
Refinement stepCycle: LAST / Resolution: 3.2→41.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14255 0 206 50 14511
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00314741
X-RAY DIFFRACTIONf_angle_d0.72320104
X-RAY DIFFRACTIONf_dihedral_angle_d17.1315464
X-RAY DIFFRACTIONf_chiral_restr0.0472398
X-RAY DIFFRACTIONf_plane_restr0.0042545
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.26530.36551310.35332521X-RAY DIFFRACTION92
3.2653-3.33630.35521290.3182578X-RAY DIFFRACTION93
3.3363-3.41390.3381420.28912565X-RAY DIFFRACTION94
3.4139-3.49920.30781290.27212602X-RAY DIFFRACTION94
3.4992-3.59380.32161350.25962602X-RAY DIFFRACTION95
3.5938-3.69940.23531400.24082610X-RAY DIFFRACTION96
3.6994-3.81880.27731380.23322609X-RAY DIFFRACTION95
3.8188-3.95510.29721410.22492606X-RAY DIFFRACTION96
3.9551-4.11340.27311290.21712654X-RAY DIFFRACTION96
4.1134-4.30040.2351320.20532695X-RAY DIFFRACTION97
4.3004-4.52680.24631190.19542664X-RAY DIFFRACTION97
4.5268-4.81010.2271450.17832669X-RAY DIFFRACTION97
4.8101-5.18080.20951540.1872679X-RAY DIFFRACTION97
5.1808-5.70090.27821670.23492639X-RAY DIFFRACTION97
5.7009-6.52310.29051480.25962684X-RAY DIFFRACTION97
6.5231-8.20760.27911500.20992657X-RAY DIFFRACTION96
8.2076-41.14320.2711530.2412646X-RAY DIFFRACTION93
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)
13.32370.2598-0.63562.510.42922.523-0.0729-0.00780.13840.01610.103-0.3028-0.110.17-0.00040.5887-0.0741-0.07240.4504-0.02020.4378-48.6104-49.31460.7923
21.8371-0.694-0.21062.69680.59752.7811-0.04170.04450.24150.02650.1019-0.4636-0.01590.2204-0.03310.2018-0.0571-0.0270.3892-0.00140.6601-106.5222-21.6055119.0242
31.0180.6715-0.97352.2055-2.23585.4399-0.18910.0993-0.0412-0.09820.1804-0.1005-0.0276-0.090.00390.37280.0632-0.03390.45920.0640.3143-32.355311.979660.0661
48.0148-2.00742.37011.5022-0.3441.0669-0.0001-0.0779-0.2713-0.21540.0292-0.0405-0.040.0985-0.05090.8355-0.20830.19440.6968-0.08430.5379-55.890811.665133.4204
51.44750.4514-1.32681.7282-0.83866.95050.19930.0392-0.11630.04580.0561-0.40730.3607-0.087-0.23960.39790.0994-0.18520.5836-0.21310.7365-90.537639.5549117.9241
66.5372-2.49190.4553.14310.06540.45020.0183-0.05830.0221-0.31490.1140.0735-0.0221-0.067-0.12080.53670.0522-0.01580.6351-0.05440.2858-114.88639.604991.2307
71.997-0.126-0.2654.94263.2254.7402-0.02970.8213-0.3313-0.95610.367-1.3273-0.00410.4334-0.59991.2605-0.37410.11440.8201-0.1980.475-52.815212.41314.0865
83.4604-1.15391.1423.2369-2.1834.4750.015-0.12850.54140.3306-0.3499-0.9880.13281.30360.38560.40350.0770.00481.1388-0.49391.4235-60.884241.8854118.7277
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 18:118 ) OR ( CHAIN B AND RESID 17:118 )A18 - 118
2X-RAY DIFFRACTION1( CHAIN A AND RESID 18:118 ) OR ( CHAIN B AND RESID 17:118 )B17 - 118
3X-RAY DIFFRACTION2( CHAIN C AND RESID 18:118 ) OR ( CHAIN D AND RESID 18:118 )C18 - 118
4X-RAY DIFFRACTION2( CHAIN C AND RESID 18:118 ) OR ( CHAIN D AND RESID 18:118 )D18 - 118
5X-RAY DIFFRACTION3( CHAIN A AND ( RESID 119:261 OR RESID 350:480 OR RESID 606:606 OR RESID 608:608 ) )A119 - 261
6X-RAY DIFFRACTION3( CHAIN A AND ( RESID 119:261 OR RESID 350:480 OR RESID 606:606 OR RESID 608:608 ) )A350 - 480
7X-RAY DIFFRACTION3( CHAIN A AND ( RESID 119:261 OR RESID 350:480 OR RESID 606:606 OR RESID 608:608 ) )A606
8X-RAY DIFFRACTION3( CHAIN A AND ( RESID 119:261 OR RESID 350:480 OR RESID 606:606 OR RESID 608:608 ) )A608
9X-RAY DIFFRACTION4( CHAIN B AND ( RESID 119:260 OR RESID 350:480 OR RESID 602:602 OR RESID 605:605 ) )B119 - 260
10X-RAY DIFFRACTION4( CHAIN B AND ( RESID 119:260 OR RESID 350:480 OR RESID 602:602 OR RESID 605:605 ) )B350 - 480
11X-RAY DIFFRACTION4( CHAIN B AND ( RESID 119:260 OR RESID 350:480 OR RESID 602:602 OR RESID 605:605 ) )B602
12X-RAY DIFFRACTION4( CHAIN B AND ( RESID 119:260 OR RESID 350:480 OR RESID 602:602 OR RESID 605:605 ) )B605
13X-RAY DIFFRACTION5( CHAIN C AND ( RESID 119:261 OR RESID 351:482 OR RESID 606:606 OR RESID 610:610 ) )C119 - 261
14X-RAY DIFFRACTION5( CHAIN C AND ( RESID 119:261 OR RESID 351:482 OR RESID 606:606 OR RESID 610:610 ) )C351 - 482
15X-RAY DIFFRACTION5( CHAIN C AND ( RESID 119:261 OR RESID 351:482 OR RESID 606:606 OR RESID 610:610 ) )C606
16X-RAY DIFFRACTION5( CHAIN C AND ( RESID 119:261 OR RESID 351:482 OR RESID 606:606 OR RESID 610:610 ) )C610
17X-RAY DIFFRACTION6( CHAIN D AND ( RESID 119:261 OR RESID 351:482 OR RESID 602:602 OR RESID 603:603 ) )D119 - 261
18X-RAY DIFFRACTION6( CHAIN D AND ( RESID 119:261 OR RESID 351:482 OR RESID 602:602 OR RESID 603:603 ) )D351 - 482
19X-RAY DIFFRACTION6( CHAIN D AND ( RESID 119:261 OR RESID 351:482 OR RESID 602:602 OR RESID 603:603 ) )D602
20X-RAY DIFFRACTION6( CHAIN D AND ( RESID 119:261 OR RESID 351:482 OR RESID 602:602 OR RESID 603:603 ) )D603
21X-RAY DIFFRACTION7( CHAIN B AND ( RESID 261:349 OR RESID 481:564 ) )B261 - 349
22X-RAY DIFFRACTION7( CHAIN B AND ( RESID 261:349 OR RESID 481:564 ) )B481 - 564
23X-RAY DIFFRACTION8( CHAIN C AND ( RESID 262:350 OR RESID 483:564 ) )C262 - 350
24X-RAY DIFFRACTION8( CHAIN C AND ( RESID 262:350 OR RESID 483:564 ) )C483 - 564

+
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