[English] 日本語
Yorodumi
- PDB-8h9y: Crystal structure of voltage-gated sodium channel NavAb N49K/L176... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8h9y
TitleCrystal structure of voltage-gated sodium channel NavAb N49K/L176Q mutant in calcium ion condition
ComponentsIon transport protein
KeywordsMEMBRANE PROTEIN / ion channel
Function / homology
Function and homology information


voltage-gated sodium channel complex / voltage-gated sodium channel activity / identical protein binding / metal ion binding
Similarity search - Function
Voltage-gated potassium channels. Chain C / Voltage-gated cation channel calcium and sodium / Helix Hairpins - #70 / Voltage-dependent channel domain superfamily / Four Helix Bundle (Hemerythrin (Met), subunit A) / Ion transport domain / Ion transport protein / Helix Hairpins / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / Ion transport protein
Similarity search - Component
Biological speciesAliarcobacter butzleri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsIrie, K. / Oda, Y.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)17K17795 Japan
Japan Society for the Promotion of Science (JSPS)20K09193 Japan
CitationJournal: Nat Commun / Year: 2023
Title: The structural basis of divalent cation block in a tetrameric prokaryotic sodium channel.
Authors: Irie, K. / Oda, Y. / Sumikama, T. / Oshima, A. / Fujiyoshi, Y.
History
DepositionOct 25, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 26, 2023Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ion transport protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,57714
Polymers31,4121
Non-polymers7,16513
Water21612
1
A: Ion transport protein
hetero molecules

A: Ion transport protein
hetero molecules

A: Ion transport protein
hetero molecules

A: Ion transport protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,30856
Polymers125,6494
Non-polymers28,65952
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area52270 Å2
ΔGint-303 kcal/mol
Surface area49070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.940, 127.940, 201.920
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422
Space group name HallI42
Symmetry operation#1: x,y,z
#2: -y,x,z
#3: y,-x,z
#4: x,-y,-z
#5: -x,y,-z
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
#9: x+1/2,y+1/2,z+1/2
#10: -y+1/2,x+1/2,z+1/2
#11: y+1/2,-x+1/2,z+1/2
#12: x+1/2,-y+1/2,-z+1/2
#13: -x+1/2,y+1/2,-z+1/2
#14: -x+1/2,-y+1/2,z+1/2
#15: y+1/2,x+1/2,-z+1/2
#16: -y+1/2,-x+1/2,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-1313-

CA

21A-1404-

HOH

31A-1408-

HOH

41A-1412-

HOH

-
Components

-
Protein / Sugars , 2 types, 3 molecules A

#1: Protein Ion transport protein / VOLTAGE-GATED SODIUM CHANNEL


Mass: 31412.252 Da / Num. of mol.: 1 / Mutation: N49K, L176Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aliarcobacter butzleri (bacteria) / Gene: Abu_1752 / Production host: Escherichia coli (E. coli) / References: UniProt: A8EVM5
#2: Sugar ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM

-
Non-polymers , 4 types, 23 molecules

#3: Chemical ChemComp-1N7 / CHAPSO / 2-hydroxy-N,N-dimethyl-3-sulfo-N-(3-{[(3beta,5beta,7beta,12beta)-3,7,12-trihydroxy-24-oxocholan-24-yl]amino}propyl)propan-1-aminium


Mass: 631.884 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C32H59N2O8S / Comment: detergent*YM
#4: Chemical
ChemComp-PX4 / 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE


Mass: 678.940 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C36H73NO8P / Comment: DMPC, phospholipid*YM
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 6.58 Å3/Da / Density % sol: 81.3 % / Description: Pyramidal shape
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 9%-11% PEG MME 2000, 100 mM sodium chloride, 100 mM magnesium nitrate, 25 mM cadmium nitrate, 100 mM Tris-HCl, pH 8.4

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 6, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.4→29.78 Å / Num. obs: 11874 / % possible obs: 92.05 % / Redundancy: 89 % / Biso Wilson estimate: 59.63 Å2 / CC1/2: 0.999 / Net I/σ(I): 17.87
Reflection shellResolution: 3.4→3.5 Å / Num. unique obs: 446 / CC1/2: 0.826

-
Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5yuc

5yuc


Resolution: 3.4→29.78 Å / SU ML: 0.3827 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 27.4084
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2636 532 4.85 %
Rwork0.2541 10432 -
obs0.2545 10964 92.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 64.47 Å2
Refinement stepCycle: LAST / Resolution: 3.4→29.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1850 0 472 12 2334
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00992367
X-RAY DIFFRACTIONf_angle_d1.24313154
X-RAY DIFFRACTIONf_chiral_restr0.0617358
X-RAY DIFFRACTIONf_plane_restr0.0063322
X-RAY DIFFRACTIONf_dihedral_angle_d23.6277998
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4-3.460.174670.2904180X-RAY DIFFRACTION32.3
3.46-3.520.3130.2761246X-RAY DIFFRACTION45.92
3.52-3.590.2608170.2714373X-RAY DIFFRACTION66.55
3.59-3.660.3145370.2639540X-RAY DIFFRACTION98.3
3.66-3.740.3027210.2526555X-RAY DIFFRACTION100
3.74-3.830.309220.2666555X-RAY DIFFRACTION99.83
3.83-3.920.2422240.2494561X-RAY DIFFRACTION100
3.92-4.030.1984190.2171576X-RAY DIFFRACTION100
4.03-4.150.1684300.2061544X-RAY DIFFRACTION100
4.15-4.280.2433350.2259554X-RAY DIFFRACTION100
4.28-4.430.2541290.2296571X-RAY DIFFRACTION100
4.44-4.610.2349270.2125567X-RAY DIFFRACTION100
4.61-4.820.2269340.2173551X-RAY DIFFRACTION99.66
4.82-5.070.273340.2364547X-RAY DIFFRACTION100
5.07-5.390.2206300.2512570X-RAY DIFFRACTION100
5.39-5.80.2963240.32574X-RAY DIFFRACTION100
5.8-6.380.3572340.3262567X-RAY DIFFRACTION100
6.38-7.290.3394260.3135588X-RAY DIFFRACTION100
7.29-9.140.2825390.2232581X-RAY DIFFRACTION99.84
9.15-29.780.2835300.2895632X-RAY DIFFRACTION99.4
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)
12.82262821834-0.2496954238990.6670690809741.6188343281-0.5111399062682.179095432310.0312657836595-0.0161896196297-0.1043912322680.370274433353-0.155826665854-0.6149938015960.3155990357080.4222830416390.246409947440.5046632951790.34238264267-0.2240176871880.7463666960580.2411055908670.60285442721235.5605477174-17.81760420828.7551501019
24.04836291366-2.167346722341.40290640824.07482724243-1.674777404652.673683842690.2645939734370.6845735154180.0469276659963-0.308629804947-0.29387523991-0.1021472871110.1290550229480.3251366081540.1202273893180.7211585176760.549332266247-0.1798200659390.8022234856480.06160313827110.68808353741335.6306062634-24.804154914626.3709433871
34.22949988134-2.339106050411.628821245764.75636472938-2.317705265491.2075671450.5912460686540.468886007485-0.865597830028-1.35449334613-0.4937300901850.1093448744641.304062831990.581407565018-0.2111290709471.374400220430.480067728482-0.2865921487390.8051707330750.1542994977210.73487802261124.0385773117-28.815856606129.8798562735
47.44926350787-0.3257949345873.917256640573.84371895441-1.002797770967.70140932130.4036440606490.492961183814-0.671957955602-0.244747810614-0.166415151322-0.6273105482231.524735829771.04443404182-0.261581853220.7199302411120.220035745768-0.06540185100230.4478332470810.2157774263040.57134181196923.8025048536-19.709286325123.5578057402
51.075534796660.459661354596-0.137824886631.609593031860.6486400954151.06371396323-0.0680153437386-0.257017322771-0.1355621280760.383207779648-0.0801663172781-0.2142529524940.4490931634920.181462838878-0.007843072583470.276820932981-0.1201923801150.0254956456320.239574364980.1463343588430.201939007079-0.214555337583-17.012777785929.1065100555
60.0299957159260.306855215919-0.2791440219564.07163519715-1.327863562664.97187265804-0.1196951482260.0728080844837-0.116714079266-0.181145490635-0.00556116495511-0.1090942148190.383318067003-0.1251957061080.1015776044540.315566325108-0.1727620092490.1434888879460.155366648048-0.02468943853550.105678493743-8.91883470738-17.26554487925.91872468443
70.8466052152090.603629617722-0.3705998539711.44479762133-0.3595673541551.01708776813-0.1493998940540.0473178708953-0.227714915726-0.0496063016701-0.005432076774270.1249444233170.206528753945-0.125664896912-0.580848903506-0.0516986258024-0.1829232842940.148551931795-0.08013210349710.06071850818280.0945936154665-8.58087057546-9.448067990812.255798331
82.82587767573-0.841871411584-0.1840466419913.225453614150.1050451866992.50000029514-0.103710178747-0.691965085240.00925820501920.842998044165-0.0355190271668-0.4269751417540.01309318389470.4516237925170.1380104506720.289162672216-0.12669898660.0303996439910.3910083260610.1788503878030.136322435126-6.45521697466-7.6352103510832.4825869912
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 999 through 1041 )999 - 10411 - 42
22chain 'A' and (resid 1042 through 1066 )1042 - 106643 - 67
33chain 'A' and (resid 1067 through 1095 )1067 - 109568 - 96
44chain 'A' and (resid 1096 through 1113 )1096 - 111397 - 114
55chain 'A' and (resid 1114 through 1152 )1114 - 1152115 - 153
66chain 'A' and (resid 1153 through 1162 )1153 - 1162154 - 163
77chain 'A' and (resid 1163 through 1193 )1163 - 1193164 - 194
88chain 'A' and (resid 1194 through 1226 )1194 - 1226195 - 227

+
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