[English] 日本語
Yorodumi
- PDB-4umo: Crystal Structure of the Kv7.1 proximal C-terminal Domain in Comp... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4umo
TitleCrystal Structure of the Kv7.1 proximal C-terminal Domain in Complex with Calmodulin
Components
  • CALMODULIN
  • POTASSIUM VOLTAGE-GATED CHANNEL SUBFAMILY KQT MEMBER 1
KeywordsSIGNALING PROTEIN / LONG QT SYNDROME
Function / homology
Function and homology information


gastrin-induced gastric acid secretion / corticosterone secretion / voltage-gated potassium channel activity involved in atrial cardiac muscle cell action potential repolarization / basolateral part of cell / lumenal side of membrane / negative regulation of voltage-gated potassium channel activity / rhythmic behavior / stomach development / iodide transport / regulation of gastric acid secretion ...gastrin-induced gastric acid secretion / corticosterone secretion / voltage-gated potassium channel activity involved in atrial cardiac muscle cell action potential repolarization / basolateral part of cell / lumenal side of membrane / negative regulation of voltage-gated potassium channel activity / rhythmic behavior / stomach development / iodide transport / regulation of gastric acid secretion / voltage-gated potassium channel activity involved in cardiac muscle cell action potential repolarization / Phase 3 - rapid repolarisation / membrane repolarization during atrial cardiac muscle cell action potential / membrane repolarization during action potential / Phase 2 - plateau phase / regulation of atrial cardiac muscle cell membrane repolarization / intracellular chloride ion homeostasis / membrane repolarization during ventricular cardiac muscle cell action potential / membrane repolarization during cardiac muscle cell action potential / negative regulation of delayed rectifier potassium channel activity / potassium ion export across plasma membrane / renal sodium ion absorption / voltage-gated potassium channel activity involved in ventricular cardiac muscle cell action potential repolarization / atrial cardiac muscle cell action potential / : / : / : / : / auditory receptor cell development / regulation of membrane repolarization / protein phosphatase 1 binding / : / positive regulation of protein autophosphorylation / detection of mechanical stimulus involved in sensory perception of sound / negative regulation of peptidyl-threonine phosphorylation / delayed rectifier potassium channel activity / ventricular cardiac muscle cell action potential / potassium ion homeostasis / Voltage gated Potassium channels / establishment of protein localization to mitochondrial membrane / positive regulation of potassium ion transmembrane transport / regulation of ventricular cardiac muscle cell membrane repolarization / type 3 metabotropic glutamate receptor binding / non-motile cilium assembly / outward rectifier potassium channel activity / cardiac muscle cell contraction / CaM pathway / positive regulation of peptidyl-threonine phosphorylation / Cam-PDE 1 activation / intestinal absorption / Sodium/Calcium exchangers / Calmodulin induced events / positive regulation of DNA binding / Reduction of cytosolic Ca++ levels / Activation of Ca-permeable Kainate Receptor / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / Loss of phosphorylation of MECP2 at T308 / CREB1 phosphorylation through the activation of Adenylate Cyclase / inner ear morphogenesis / response to corticosterone / CaMK IV-mediated phosphorylation of CREB / PKA activation / negative regulation of high voltage-gated calcium channel activity / Glycogen breakdown (glycogenolysis) / CLEC7A (Dectin-1) induces NFAT activation / Activation of RAC1 downstream of NMDARs / negative regulation of ryanodine-sensitive calcium-release channel activity / organelle localization by membrane tethering / adrenergic receptor signaling pathway / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / negative regulation of calcium ion export across plasma membrane / regulation of cardiac muscle cell action potential / ciliary base / renal absorption / regulation of heart contraction / presynaptic endocytosis / protein kinase A regulatory subunit binding / nitric-oxide synthase binding / Synthesis of IP3 and IP4 in the cytosol / protein kinase A catalytic subunit binding / regulation of synaptic vesicle exocytosis / regulation of cell communication by electrical coupling involved in cardiac conduction / Phase 0 - rapid depolarisation / potassium ion import across plasma membrane / calcineurin-mediated signaling / Negative regulation of NMDA receptor-mediated neuronal transmission / Unblocking of NMDA receptors, glutamate binding and activation / inner ear development / RHO GTPases activate PAKs / regulation of heart rate by cardiac conduction / Ion transport by P-type ATPases / Uptake and function of anthrax toxins / adenylate cyclase binding / action potential / regulation of ryanodine-sensitive calcium-release channel activity / protein phosphatase activator activity / Long-term potentiation / cochlea development / Calcineurin activates NFAT
Similarity search - Function
Helix Hairpins - #1910 / Potassium channel, voltage dependent, KCNQ1 / Potassium channel, voltage dependent, KCNQ / Potassium channel, voltage dependent, KCNQ, C-terminal / KCNQ voltage-gated potassium channel / Helix Hairpins / Voltage-dependent channel domain superfamily / : / Helix non-globular / EF-hand domain pair ...Helix Hairpins - #1910 / Potassium channel, voltage dependent, KCNQ1 / Potassium channel, voltage dependent, KCNQ / Potassium channel, voltage dependent, KCNQ, C-terminal / KCNQ voltage-gated potassium channel / Helix Hairpins / Voltage-dependent channel domain superfamily / : / Helix non-globular / EF-hand domain pair / Special / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / Ion transport domain / Ion transport protein / EF-hand domain pair
Similarity search - Domain/homology
: / THIOCYANATE ION / Calmodulin-1 / Potassium voltage-gated channel subfamily KQT member 1 / Calmodulin-3
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3 Å
AuthorsSachyani, D. / Hirsch, J.A.
CitationJournal: Structure / Year: 2014
Title: Structural Basis of a Kv7.1 Potassium Channel Gating Module: Studies of the Intracellular C-Terminal Domain in Complex with Calmodulin
Authors: Sachyani, D. / Dvir, M. / Strulovich, R. / Tria, G. / Tobelaim, W. / Peretz, A. / Pongs, O. / Svergun, D. / Attali, B. / Hirsch, J.A.
History
DepositionMay 20, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 5, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 17, 2014Group: Database references
Revision 1.2Apr 3, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_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_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_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: POTASSIUM VOLTAGE-GATED CHANNEL SUBFAMILY KQT MEMBER 1
B: POTASSIUM VOLTAGE-GATED CHANNEL SUBFAMILY KQT MEMBER 1
C: CALMODULIN
D: CALMODULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,95613
Polymers60,5814
Non-polymers3759
Water181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13510 Å2
ΔGint-137.8 kcal/mol
Surface area23790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)151.760, 151.760, 56.091
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

-
Components

-
Protein , 2 types, 4 molecules ABCD

#1: Protein POTASSIUM VOLTAGE-GATED CHANNEL SUBFAMILY KQT MEMBER 1 / KV7.1 CHANNEL / IKS PRODUCING SLOW VOLTAGE-GATED POTASSIUM CHANNEL SUBUNIT ALPHA KVLQT1 / KQT-LIKE ...KV7.1 CHANNEL / IKS PRODUCING SLOW VOLTAGE-GATED POTASSIUM CHANNEL SUBUNIT ALPHA KVLQT1 / KQT-LIKE 1 / VOLTAGE-GATED POTASSIUM CHANNEL SUBUNIT KV7.1


Mass: 13438.191 Da / Num. of mol.: 2
Fragment: PROXIMAL C-TERMINAL DOMAIN, RESIDUES 352-396,502-539
Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET DUET / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P51787
#2: Protein CALMODULIN / CAM


Mass: 16852.545 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET DUET / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P62158, UniProt: P0DP23*PLUS

-
Non-polymers , 4 types, 10 molecules

#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CNS
#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 3.08 Å3/Da / Density % sol: 60.06 % / Description: NONE
Crystal growTemperature: 277 K
Details: 0.3 M POTASSIUM THIOCYANATE, 0.1 M SODIUM ACETATE TRIHYDRATE PH=5.6, 1 MM EGTA AT 4 DEGREES CELSIUS

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.974
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.974 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 15107 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 13.1 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 40.8

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.9_1692)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 3→49.675 Å / SU ML: 0.33 / σ(F): 1.34 / Phase error: 28.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2466 757 5 %
Rwork0.2133 --
obs0.215 15006 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3→49.675 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3506 0 11 1 3518
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053594
X-RAY DIFFRACTIONf_angle_d0.8944813
X-RAY DIFFRACTIONf_dihedral_angle_d14.9421282
X-RAY DIFFRACTIONf_chiral_restr0.036528
X-RAY DIFFRACTIONf_plane_restr0.004645
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0002-3.23180.32351590.2822795X-RAY DIFFRACTION100
3.2318-3.5570.2651460.24222836X-RAY DIFFRACTION100
3.557-4.07150.23711510.21332821X-RAY DIFFRACTION100
4.0715-5.12880.23021470.19092868X-RAY DIFFRACTION100
5.1288-49.68190.23771540.20452929X-RAY DIFFRACTION100
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)
16.11550.32980.80610.00210.08945.95380.25110.30050.08460.37920.003-0.0101-0.46020.1619-0.16670.71640.0699-0.12610.2983-0.13740.479852.3230.873831.0243
27.5081-5.14196.19089.3658-5.66138.5934-0.3487-0.59970.362-0.55390.6935-0.26450.1514-0.4046-0.20430.45680.20660.08830.7772-0.05420.298422.922746.75156.9513
34.4254-2.55474.61081.908-1.77673.7659-0.20940.43920.33240.0996-0.05240.405-0.3550.4070.38950.3327-0.0503-0.00040.56640.11480.73473.973867.4757-2.749
47.1954-5.35.42695.8756-5.77448.84180.48460.0147-0.18410.4646-0.0977-0.0420.1742-0.16930.04150.57370.2698-0.04990.4975-0.1320.24638.588735.752731.0347
58.6485-3.2674-4.61946.96691.68172.4433-0.3304-1.30790.2112-0.77270.4633-0.8261.11121.4671-0.18350.79740.0842-0.00430.8766-0.16260.429231.340537.00210.2373
65.8603-3.0065-4.93473.13411.23695.2128-0.21320.2205-0.23370.1416-1.50221.27532.5553-1.25641.60911.185-0.277-0.25520.89390.05980.805818.004930.55131.1249
73.3181-1.74282.25985.7880.53267.1768-0.018-1.63020.09321.3374-0.05481.41090.786-1.53040.03850.4626-0.03010.15670.78730.06350.548813.929439.0711.0781
86.5609-2.1021-5.18396.66311.73375.51230.62470.46381.1269-0.7543-0.01480.4623-0.1244-1.2079-0.39030.35510.0746-0.16640.8118-0.12810.437711.524644.3941.5408
96.25530.04816.55352.0402-1.11018.6550.28522.8385-0.9505-3.12260.46591.22271.8182-1.5543-0.76120.97490.0116-0.30971.12950.07150.764714.948638.4179-6.9899
106.2741.1167-2.67514.7223.1876.56250.01690.91080.5505-1.67220.46510.4928-1.1335-0.6412-0.43850.64610.30760.12920.8829-0.06110.364825.672144.9976-3.7199
113.2198-3.003-3.42814.42214.91196.31250.9383-0.38710.5519-0.8588-0.4788-0.1571-1.13920.9457-0.40140.7676-0.1230.16530.7603-0.00710.76223.213464.97560.5173
123.44390.26782.18883.6816-2.13523.03680.24490.33231.0379-0.5737-0.5236-1.122-3.19172.7333-0.10191.4536-0.41710.54311.15740.09351.246618.524473.77978.6581
135.11430.9914-4.18260.6202-1.99236.64690.4454-1.19231.50040.7341-0.12931.2324-1.76371.7802-0.2690.5618-0.0923-0.00880.5288-0.15730.931919.297466.633217.0742
148.2673-4.04983.39365.2309-5.35418.5167-1.3105-1.15470.98560.3360.6105-0.51381.1598-1.3466-0.74230.4612-0.0348-0.08140.8781-0.10130.584716.004955.980316.0268
152.00099.5989-5.32439.8382-3.95224.59571.3365-2.9038-0.95433.0145-2.0508-2.06610.04171.37990.37920.6582-0.0501-0.27261.1981-0.28890.909727.104359.613520.005
160.18320.9375-1.30514.7835-6.65179.2483-0.4771-0.48060.52961.2646-0.6109-2.1916-1.22572.65950.49420.777-0.0919-0.17731.4757-0.41121.918430.958572.796318.3598
172.7834-4.02631.77498.1738-0.02343.88460.90260.63142.8659-0.21250.1277-1.7512-1.73341.3122-0.86040.1012-0.20280.30310.8259-0.17141.466329.581266.19157.9427
188.9082-1.6733-2.64927.51613.11532.3188-0.1761-0.50030.7905-0.11220.4244-0.3432-0.6170.1577-0.08080.92460.30260.09111.0048-0.04410.480729.127737.586140.0013
197.0836-2.7492-0.97925.81740.62468.4576-0.3056-0.6402-0.72140.6180.5855-0.27560.882-0.2363-0.32210.82210.18570.02630.39210.03810.398736.125.601239.7335
204.204-5.21980.65616.85760.34143.03730.4447-1.6566-0.21970.10230.5498-1.271-1.2131.846-1.28191.1118-0.2076-0.36980.9213-0.36821.482661.936435.702537.2504
214.26585.0435-1.52196.98410.73247.23850.03311.17281.0695-1.06910.0081-1.3961-0.41980.0217-0.2630.49060.07210.15170.37570.09211.009455.98134.710922.9225
223.39550.9320.25851.48810.13021.1848-0.62480.3921.247-0.93430.7384-0.7606-0.93180.50250.3490.4582-0.60220.03150.1161-0.46121.942460.371943.757729.9485
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 356 THROUGH 395 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 396 THROUGH 535 )
3X-RAY DIFFRACTION3CHAIN 'B' AND (RESID 328 THROUGH 385 )
4X-RAY DIFFRACTION4CHAIN 'B' AND (RESID 386 THROUGH 535 )
5X-RAY DIFFRACTION5CHAIN 'C' AND (RESID 3 THROUGH 19 )
6X-RAY DIFFRACTION6CHAIN 'C' AND (RESID 20 THROUGH 28 )
7X-RAY DIFFRACTION7CHAIN 'C' AND (RESID 29 THROUGH 44 )
8X-RAY DIFFRACTION8CHAIN 'C' AND (RESID 45 THROUGH 55 )
9X-RAY DIFFRACTION9CHAIN 'C' AND (RESID 56 THROUGH 64 )
10X-RAY DIFFRACTION10CHAIN 'C' AND (RESID 65 THROUGH 77 )
11X-RAY DIFFRACTION11CHAIN 'C' AND (RESID 78 THROUGH 90 )
12X-RAY DIFFRACTION12CHAIN 'C' AND (RESID 91 THROUGH 98 )
13X-RAY DIFFRACTION13CHAIN 'C' AND (RESID 99 THROUGH 111 )
14X-RAY DIFFRACTION14CHAIN 'C' AND (RESID 112 THROUGH 117 )
15X-RAY DIFFRACTION15CHAIN 'C' AND (RESID 118 THROUGH 128 )
16X-RAY DIFFRACTION16CHAIN 'C' AND (RESID 129 THROUGH 134 )
17X-RAY DIFFRACTION17CHAIN 'C' AND (RESID 135 THROUGH 147 )
18X-RAY DIFFRACTION18CHAIN 'D' AND (RESID 5 THROUGH 19 )
19X-RAY DIFFRACTION19CHAIN 'D' AND (RESID 20 THROUGH 78 )
20X-RAY DIFFRACTION20CHAIN 'D' AND (RESID 79 THROUGH 98 )
21X-RAY DIFFRACTION21CHAIN 'D' AND (RESID 99 THROUGH 128 )
22X-RAY DIFFRACTION22CHAIN 'D' AND (RESID 129 THROUGH 147 )

+
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