[English] 日本語
Yorodumi
- PDB-6c1p: HypoPP mutant -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6c1p
TitleHypoPP mutant
ComponentsIon transport protein
KeywordsMETAL TRANSPORT / Mutant
Function / homology
Function and homology information


voltage-gated sodium channel complex / voltage-gated sodium channel activity / metal ion binding / identical protein binding
Similarity search - Function
Voltage-gated cation channel calcium and sodium / Voltage-dependent channel domain superfamily / Ion transport domain / Ion transport protein
Similarity search - Domain/homology
PHOSPHATE ION / 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / Ion transport protein
Similarity search - Component
Biological speciesArcobacter butzleri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsCatterall, W.A. / Zheng, N. / Jiang, D. / Gamal El-Din, T.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)NS015751 United States
Citation
Journal: Nature / Year: 2018
Title: Structural basis for gating pore current in periodic paralysis.
Authors: Jiang, D. / Gamal El-Din, T.M. / Ing, C. / Lu, P. / Pomes, R. / Zheng, N. / Catterall, W.A.
#1: Journal: Nature / Year: 2011
Title: The crystal structure of a voltage-gated sodium channel.
Authors: Catterall, W.A. / Zheng, N. / Payandeh, J.
History
DepositionJan 5, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2018Provider: repository / Type: Initial release
Revision 1.1May 30, 2018Group: Data collection / Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jun 6, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 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: Ion transport protein
B: Ion transport protein
C: Ion transport protein
D: Ion transport protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,02622
Polymers132,0204
Non-polymers11,00618
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22400 Å2
ΔGint-149 kcal/mol
Surface area44180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.500, 125.552, 192.045
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221

-
Components

#1: Protein
Ion transport protein


Mass: 33004.949 Da / Num. of mol.: 4 / Mutation: C235I, H123R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arcobacter butzleri (strain RM4018) (bacteria)
Strain: RM4018 / Gene: Abu_1752 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A8EVM5
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: PO4
#3: Chemical
ChemComp-PX4 / 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE


Mass: 678.940 Da / Num. of mol.: 15
Source method: isolated from a genetically manipulated source
Formula: C36H73NO8P / Comment: DMPC, phospholipid*YM
#4: 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

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 5.73 Å3/Da / Density % sol: 78.53 %
Crystal growTemperature: 277 K / Method: evaporation / Details: ammonium sulphate, Na-citrate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.99994 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Sep 26, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99994 Å / Relative weight: 1
ReflectionResolution: 2.8→48.46 Å / Num. obs: 67766 / % possible obs: 98 % / Redundancy: 5.1 % / Net I/σ(I): 14.5
Reflection shellResolution: 2.8→2.9 Å

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
AutoSolphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3rvy

3rvy


Resolution: 2.9→48.458 Å / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.66 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2603 3444 5.08 %
Rwork0.2355 --
obs0.2388 67766 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.9→48.458 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7138 0 405 0 7543
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0127764
X-RAY DIFFRACTIONf_angle_d1.70310527
X-RAY DIFFRACTIONf_dihedral_angle_d16.7142743
X-RAY DIFFRACTIONf_chiral_restr0.0971228
X-RAY DIFFRACTIONf_plane_restr0.0081206
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9004-2.95040.32671640.31943084X-RAY DIFFRACTION93
2.9504-3.0040.30481760.32823153X-RAY DIFFRACTION94
3.004-3.06170.39081780.3253215X-RAY DIFFRACTION95
3.0617-3.12420.3441390.31863171X-RAY DIFFRACTION96
3.1242-3.1920.32971710.31223204X-RAY DIFFRACTION95
3.192-3.26620.29311780.29623155X-RAY DIFFRACTION95
3.2662-3.34780.31621890.29173152X-RAY DIFFRACTION94
3.3478-3.43830.29981680.28563209X-RAY DIFFRACTION95
3.4383-3.53930.31061490.28893229X-RAY DIFFRACTION96
3.5393-3.65340.27061850.26723145X-RAY DIFFRACTION94
3.6534-3.78380.29451800.25683213X-RAY DIFFRACTION95
3.7838-3.93510.26521680.2333213X-RAY DIFFRACTION95
3.9351-4.11380.24461730.22063191X-RAY DIFFRACTION95
4.1138-4.33030.25781680.23673255X-RAY DIFFRACTION95
4.3303-4.60090.24731750.21413222X-RAY DIFFRACTION95
4.6009-4.9550.23631690.20013202X-RAY DIFFRACTION95
4.955-5.45160.24081840.21283268X-RAY DIFFRACTION95
5.4516-6.23570.2911750.24043240X-RAY DIFFRACTION95
6.2357-7.83850.28851650.24763321X-RAY DIFFRACTION95
7.8385-32.73420.20331840.19313435X-RAY DIFFRACTION95
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)
14.41351.73675.01794.4123.61176.4217-0.21220.50140.11480.47690.5844-0.9547-0.58130.7152-0.25352.6166-0.2784-0.25382.1125-0.99481.202136.7774-67.183236.8437
26.0078-0.0529-0.19522.2023-2.75083.61690.1294-0.84821.00330.08821.6004-0.1816-1.1681.5231-0.67861.0994-0.0980.16110.6066-0.56831.419722.9559-66.8263219.7565
31.822-0.7625-0.07854.7581-4.2674.19090.6229-0.28051.0663-0.16670.33930.06430.46180.2763-0.11961.4847-0.5219-0.26091.0143-0.67231.54831.4591-70.1509218.524
46.37192.83825.30525.78451.94556.0455-0.23870.77790.00520.10451.0307-1.6496-0.16681.3118-0.35961.0771-0.2351-0.20931.485-0.73671.278428.664-79.1291217.0165
51.4203-0.0002-1.0063.51580.5343.76580.4884-1.11240.16510.5181-0.5515-0.1004-0.6327-0.0938-0.01280.872-0.2649-0.11641.4236-0.03030.604215.1343-98.971221.5679
63.62480.70262.60136.60660.23382.16481.08190.9819-0.0751-0.5809-0.7994-0.94820.18220.33020.30150.84610.288-0.01060.96840.3560.489412.9282-108.1565197.7271
78.78481.1686-2.17524.0290.97781.28950.0981-0.5011-0.3539-0.11120.1672-0.2508-0.78460.0008-0.30990.6948-0.05990.00890.57480.08260.28478.16-101.7772206.9603
86.1921-0.92320.57452.7856-0.95370.57250.50820.098-2.1315-0.4678-0.16340.29680.36480.1342-0.66160.8886-0.2669-0.34570.5583-0.0250.57341.838-110.484198.1839
93.7224-1.3509-0.84271.9655-0.65952.1287-0.0065-1.4884-0.2280.48360.05850.34310.27180.4406-0.39151.4553-0.2282-0.45540.93670.2780.3213.3902-106.4371218.3595
107.61273.9785-5.91335.4591-2.45445.0569-0.41941.2115-1.1328-1.65161.3672-1.3877-0.56940.5578-0.68921.24450.0902-0.13082.6467-0.88621.278426.5184-133.3898235.6635
116.76152.3771-3.57682.44390.10373.0423-0.6025-0.65240.04830.3248-1.12410.23811.10781.70561.13531.03360.2776-0.09120.99370.21410.755926.335-118.6721219.6706
121.97810.41060.44173.7198-1.12391.6007-0.2113-0.5695-1.332-0.2848-0.0393-0.37490.4068-0.36180.09381.24690.1107-0.58671.16840.29951.213920.443-126.5273219.34
132.39381.25521.56522.12421.25358.3993-0.915-1.1786-1.48610.3258-0.8978-0.2080.41581.09371.2630.68210.1230.05921.21080.41791.334715.6772-121.9167215.4258
140.911-0.84980.89671.0071-0.56041.4059-0.671-0.7585-0.96650.78820.09720.2025-0.54490.3409-0.16571.0719-0.1508-0.15141.35250.53730.5175-7.7746-110.5684219.7712
152.3809-3.85410.24546.3731-1.21915.0320.84160.207-0.7646-1.428-0.12210.85111.9724-1.0001-1.18531.3845-0.0679-0.35230.57910.18770.2491-13.9302-107.8161196.7438
164.8909-1.59090.46575.99891.77515.33710.5762-0.5471-0.71530.0434-0.47030.4405-0.31930.4036-0.21010.555-0.215-0.00910.54870.07580.3711-8.1448-103.4496206.0532
172.7883-0.4911-0.90223.69550.10436.0383-0.2826-0.420.0042-0.22490.54820.08320.2925-0.351-0.29660.8044-0.43740.02630.88150.04250.4102-13.9042-98.5044212.8883
188.6315-3.7851-2.37055.1458-3.75477.24310.0785-1.14210.97750.55080.4386-0.8006-1.24460.9864-0.50531.79520.95920.19262.7780.03930.8757-30.0792-54.5143233.735
191.7769-0.9576-0.34247.59115.31413.75990.4103-0.2090.3443-0.226-0.13610.0897-1.7872-0.95020.17321.430.34210.4941.1892-0.24341.1863-28.1781-65.7467213.6618
203.1439-1.1613-2.0582.39942.96963.8182-0.1677-1.26160.36080.0381-0.17330.08970.0188-0.0843-0.59012.10990.64841.32381.5944-0.18551.6097-15.8722-56.279230.5403
219.5573-1.3041.53312.75512.31023.40240.27471.11290.61330.457-0.86150.6838-0.7533-0.72940.60860.89040.18680.01411.3392-0.63081.2762-15.0819-60.9635214.3401
224.054-2.75131.48786.49974.05926.1172-0.219-1.16011.9385-0.45470.551-0.8036-1.916-0.9358-0.28060.9540.01060.08350.8119-0.26520.9627-18.0078-68.2399214.7156
233.49561.3618-1.13974.1848-0.99592.1751-0.3999-1.7410.1818-1.1841-0.6426-0.27480.5702-1.14481.07331.75-0.00280.32451.2563-0.26330.6584-13.7109-76.4848229.5018
241.7685-0.22771.97734.64081.67243.0084-0.2732-0.2430.02140.5135-0.08490.54090.01450.18440.12230.8944-0.23040.13660.6973-0.40320.962312.7272-78.7771216.0076
258.0887-0.27811.97367.71373.81262.4421-0.2252-0.17621.9041-1.16520.29110.0446-1.9190.8514-0.39381.3777-0.12320.21520.5475-0.19450.652713.2986-80.7849197.6754
268.0004-1.2808-0.16453.15393.13333.27630.2509-0.68731.00010.0359-0.2564-0.20980.1611-0.9373-0.16460.7346-0.0390.07390.713-0.09090.39776.7743-85.7239206.5342
276.44666.196-6.5348.7294-7.96847.6516-0.14530.18420.36-1.59890.8405-0.27271.3255-0.2452-0.44190.7171-0.2750.12450.6552-0.03650.353515.9501-91.8698198.9589
281.453-1.0049-0.19082.5244-0.92381.7120.1463-0.2968-0.36620.9448-0.0493-0.08580.1271-1.0139-0.20520.9849-0.3107-0.10461.2072-0.21770.654210.7095-89.9154218.607
294.38660.5854-2.62536.03790.79874.94290.5642-0.533-1.40980.1650.40480.88440.3738-1.1007-0.10551.057-0.3509-0.02451.26360.76731.2964-32.6738-117.3887218.1214
303.1099-0.1547-0.41633.26850.81492.78590.2876-1.1010.42890.39740.15260.1931-0.1304-0.0222-0.41320.62-0.05760.14640.8799-0.01730.4068-13.4004-88.8319212.6769
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1001 through 1011 )
2X-RAY DIFFRACTION2chain 'A' and (resid 1012 through 1034 )
3X-RAY DIFFRACTION3chain 'A' and (resid 1035 through 1073 )
4X-RAY DIFFRACTION4chain 'A' and (resid 1074 through 1112 )
5X-RAY DIFFRACTION5chain 'A' and (resid 1113 through 1152 )
6X-RAY DIFFRACTION6chain 'A' and (resid 1153 through 1162 )
7X-RAY DIFFRACTION7chain 'A' and (resid 1163 through 1183 )
8X-RAY DIFFRACTION8chain 'A' and (resid 1184 through 1191 )
9X-RAY DIFFRACTION9chain 'A' and (resid 1192 through 1219 )
10X-RAY DIFFRACTION10chain 'B' and (resid 1001 through 1011 )
11X-RAY DIFFRACTION11chain 'B' and (resid 1012 through 1034 )
12X-RAY DIFFRACTION12chain 'B' and (resid 1035 through 1088 )
13X-RAY DIFFRACTION13chain 'B' and (resid 1089 through 1115 )
14X-RAY DIFFRACTION14chain 'B' and (resid 1116 through 1152 )
15X-RAY DIFFRACTION15chain 'B' and (resid 1153 through 1162 )
16X-RAY DIFFRACTION16chain 'B' and (resid 1163 through 1183 )
17X-RAY DIFFRACTION17chain 'B' and (resid 1184 through 1219 )
18X-RAY DIFFRACTION18chain 'C' and (resid 1001 through 1011 )
19X-RAY DIFFRACTION19chain 'C' and (resid 1012 through 1065 )
20X-RAY DIFFRACTION20chain 'C' and (resid 1066 through 1074 )
21X-RAY DIFFRACTION21chain 'C' and (resid 1075 through 1096 )
22X-RAY DIFFRACTION22chain 'C' and (resid 1097 through 1112 )
23X-RAY DIFFRACTION23chain 'C' and (resid 1113 through 1127 )
24X-RAY DIFFRACTION24chain 'C' and (resid 1128 through 1152 )
25X-RAY DIFFRACTION25chain 'C' and (resid 1153 through 1162 )
26X-RAY DIFFRACTION26chain 'C' and (resid 1163 through 1183 )
27X-RAY DIFFRACTION27chain 'C' and (resid 1184 through 1191 )
28X-RAY DIFFRACTION28chain 'C' and (resid 1192 through 1219 )
29X-RAY DIFFRACTION29chain 'D' and (resid 1001 through 1096 )
30X-RAY DIFFRACTION30chain 'D' and (resid 1097 through 1219 )

+
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