[English] 日本語
Yorodumi
- PDB-5nin: Crystal Structure of AKAP79 calmodulin binding domain peptide in ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5nin
TitleCrystal Structure of AKAP79 calmodulin binding domain peptide in complex with Ca2+/Calmodulin
Components
  • A-kinase anchor protein 5
  • Calmodulin
KeywordsSIGNALING PROTEIN / Calmodulin / Calcium / AKAP79 / AKAP150 / AKAP5 / AKAP / EF hand / Ca2+
Function / homology
Function and homology information


positive regulation of endosome to plasma membrane protein transport / regulation of protein kinase A signaling / postsynaptic recycling endosome membrane / postsynaptic recycling endosome / positive regulation of calcium ion import across plasma membrane / ROBO receptors bind AKAP5 / protein serine/threonine phosphatase complex / calcineurin-NFAT signaling cascade / : / : ...positive regulation of endosome to plasma membrane protein transport / regulation of protein kinase A signaling / postsynaptic recycling endosome membrane / postsynaptic recycling endosome / positive regulation of calcium ion import across plasma membrane / ROBO receptors bind AKAP5 / protein serine/threonine phosphatase complex / calcineurin-NFAT signaling cascade / : / : / positive regulation of cyclic-nucleotide phosphodiesterase activity / : / GABA receptor binding / establishment of protein localization to mitochondrial membrane / positive regulation of calcineurin-NFAT signaling cascade / negative regulation of peptidyl-threonine phosphorylation / type 3 metabotropic glutamate receptor binding / negative regulation of adenylate cyclase activity / protein phosphatase 2B binding / Trafficking of AMPA receptors / CaM pathway / Cam-PDE 1 activation / beta-2 adrenergic receptor binding / Sodium/Calcium exchangers / Calmodulin induced events / 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 / positive regulation of DNA binding / PKA activation / CaMK IV-mediated phosphorylation of CREB / negative regulation of high voltage-gated calcium channel activity / response to corticosterone / positive regulation of peptidyl-threonine phosphorylation / Glycogen breakdown (glycogenolysis) / CLEC7A (Dectin-1) induces NFAT activation / Activation of RAC1 downstream of NMDARs / nitric-oxide synthase binding / protein kinase A binding / negative regulation of calcium ion export across plasma membrane / organelle localization by membrane tethering / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / regulation of synaptic vesicle exocytosis / presynaptic endocytosis / regulation of cardiac muscle cell action potential / positive regulation of ryanodine-sensitive calcium-release channel activity / Synthesis of IP3 and IP4 in the cytosol / protein kinase A regulatory subunit binding / regulation of cell communication by electrical coupling involved in cardiac conduction / Phase 0 - rapid depolarisation / Negative regulation of NMDA receptor-mediated neuronal transmission / negative regulation of ryanodine-sensitive calcium-release channel activity / Unblocking of NMDA receptors, glutamate binding and activation / RHO GTPases activate PAKs / calcineurin-mediated signaling / regulation of synaptic vesicle endocytosis / Ion transport by P-type ATPases / positive regulation of protein autophosphorylation / Uptake and function of anthrax toxins / Long-term potentiation / Regulation of MECP2 expression and activity / Calcineurin activates NFAT / protein phosphatase activator activity / adenylate cyclase binding / regulation of ryanodine-sensitive calcium-release channel activity / excitatory synapse / DARPP-32 events / Smooth Muscle Contraction / catalytic complex / detection of calcium ion / regulation of cardiac muscle contraction / positive regulation of protein serine/threonine kinase activity / glutamate receptor binding / RHO GTPases activate IQGAPs / phosphatidylinositol 3-kinase binding / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / presynaptic cytosol / calcium channel inhibitor activity / cellular response to interferon-beta / Protein methylation / Activation of AMPK downstream of NMDARs / Ion homeostasis / activation of adenylate cyclase activity / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / eNOS activation / enzyme regulator activity / regulation of calcium-mediated signaling / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / titin binding / voltage-gated potassium channel complex / dendrite membrane / sperm midpiece / substantia nigra development / calcium channel complex / calyx of Held / nitric-oxide synthase regulator activity / FCERI mediated Ca+2 mobilization
Similarity search - Function
A kinase-anchoring protein AKAP5 and AKAP12, calmodulin (CaM)-binding motif / A-kinase anchor protein 5 / WSK motif / A kinase-anchoring proteins AKAP-5 and AKAP-12 calmodulin (CaM)-binding motif profile. / EF-hand / : / Recoverin; domain 1 / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site ...A kinase-anchoring protein AKAP5 and AKAP12, calmodulin (CaM)-binding motif / A-kinase anchor protein 5 / WSK motif / A kinase-anchoring proteins AKAP-5 and AKAP-12 calmodulin (CaM)-binding motif profile. / EF-hand / : / Recoverin; domain 1 / EF-hand domain pair / 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 / EF-hand domain pair / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Calmodulin-1 / A-kinase anchor protein 5 / Calmodulin-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsGold, M.G. / Patel, N.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Wellcome Trust104194/Z/14/Z United Kingdom
Royal Society104194/Z/14/Z United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/N015274/1 United Kingdom
CitationJournal: Nat Commun / Year: 2017
Title: Molecular basis of AKAP79 regulation by calmodulin.
Authors: Patel, N. / Stengel, F. / Aebersold, R. / Gold, M.G.
History
DepositionMar 24, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 6, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Calmodulin
A: Calmodulin
C: A-kinase anchor protein 5
D: A-kinase anchor protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,12813
Polymers37,4884
Non-polymers6419
Water8,989499
1
B: Calmodulin
D: A-kinase anchor protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3049
Polymers18,7442
Non-polymers5607
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2560 Å2
ΔGint-86 kcal/mol
Surface area8540 Å2
MethodPISA
2
A: Calmodulin
C: A-kinase anchor protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8244
Polymers18,7442
Non-polymers802
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1800 Å2
ΔGint-39 kcal/mol
Surface area8490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.460, 76.460, 128.990
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

-
Components

#1: 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)
Gene: CALM1, CALM, CAM, CAM1, CALM2, CAM2, CAMB, CALM3, CALML2, CAM3, CAMC, CAMIII
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P62158, UniProt: P0DP23*PLUS
#2: Protein/peptide A-kinase anchor protein 5 / AKAP-5 / A-kinase anchor protein 79 kDa / AKAP 79 / H21 / cAMP-dependent protein kinase regulatory ...AKAP-5 / A-kinase anchor protein 79 kDa / AKAP 79 / H21 / cAMP-dependent protein kinase regulatory subunit II high affinity-binding protein


Mass: 1891.273 Da / Num. of mol.: 2 / Fragment: UNP residues 77-92 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P24588
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 499 / 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: 2.51 Å3/Da / Density % sol: 51.08 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 5.4
Details: 2.4 M ammonium sulphate, 50 mM citrate pH 5.4, 0.3 M NDSB-195

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9685 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 22, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9685 Å / Relative weight: 1
ReflectionResolution: 1.7→65.77 Å / Num. obs: 42359 / % possible obs: 99.1 % / Redundancy: 7.4 % / CC1/2: 0.99 / Rpim(I) all: 0.063 / Net I/σ(I): 10.1
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 7.5 % / Mean I/σ(I) obs: 3.1 / Num. unique obs: 2193 / CC1/2: 0.552 / Rpim(I) all: 0.354 / % possible all: 99.6

-
Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1IWQ (85-148)

1iwq


Resolution: 1.7→54.065 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.93
RfactorNum. reflection% reflectionSelection details
Rfree0.1944 3860 4.94 %random selection
Rwork0.1644 ---
obs0.1659 42303 97.32 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.7→54.065 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2394 0 29 499 2922
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092465
X-RAY DIFFRACTIONf_angle_d0.9043319
X-RAY DIFFRACTIONf_dihedral_angle_d10.6681501
X-RAY DIFFRACTIONf_chiral_restr0.052370
X-RAY DIFFRACTIONf_plane_restr0.005438
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.72070.25851110.23872659X-RAY DIFFRACTION98
1.7207-1.74250.2631590.22552660X-RAY DIFFRACTION98
1.7425-1.76550.26861240.23072670X-RAY DIFFRACTION99
1.7655-1.78960.22991320.21852715X-RAY DIFFRACTION98
1.7896-1.81520.28271130.2182734X-RAY DIFFRACTION98
1.8152-1.84230.21051510.20262639X-RAY DIFFRACTION98
1.8423-1.87110.24251160.19492691X-RAY DIFFRACTION98
1.8711-1.90180.23381340.20542690X-RAY DIFFRACTION98
1.9018-1.93460.25871300.18832680X-RAY DIFFRACTION98
1.9346-1.96970.19951230.17952703X-RAY DIFFRACTION98
1.9697-2.00760.1971510.1632647X-RAY DIFFRACTION98
2.0076-2.04860.17871480.15872615X-RAY DIFFRACTION97
2.0486-2.09320.18661540.15792675X-RAY DIFFRACTION98
2.0932-2.14190.19381620.14642661X-RAY DIFFRACTION98
2.1419-2.19540.15331280.14252638X-RAY DIFFRACTION97
2.1954-2.25480.16171500.13992636X-RAY DIFFRACTION97
2.2548-2.32110.18981030.13342666X-RAY DIFFRACTION97
2.3211-2.3960.15971470.13712648X-RAY DIFFRACTION97
2.396-2.48170.20781800.13962586X-RAY DIFFRACTION96
2.4817-2.5810.14681170.13732678X-RAY DIFFRACTION97
2.581-2.69850.17531360.13662640X-RAY DIFFRACTION97
2.6985-2.84080.18261540.14322659X-RAY DIFFRACTION97
2.8408-3.01870.21131480.15722598X-RAY DIFFRACTION96
3.0187-3.25180.1881360.1532642X-RAY DIFFRACTION97
3.2518-3.5790.18591250.14642682X-RAY DIFFRACTION97
3.579-4.09670.1581370.13862642X-RAY DIFFRACTION97
4.0967-5.16080.17661450.1612615X-RAY DIFFRACTION96
5.1608-54.09270.23261460.23432578X-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)
10.0162-0.0135-0.00040.0607-0.01030.00690.0038-0.074-0.0168-0.0394-0.00960.05440.0099-0.0019-0.00090.05290.01890.01150.06590.0010.05116.8674-26.9563-27.8416
20.0182-0.0026-0.00290.0014-0.00090.0042-0.0350.01310.0057-0.00940.0035-0.001-0.01230.0014-0.00010.11440.0153-0.0010.072-0.02130.07371.1044-21.5112-41.0999
30.0143-0.0148-0.0060.05220.01220.01990.04450.00510.0160.0194-0.0064-0.0188-0.078-0.00950.00170.0306-0.00530.01380.0263-0.00420.05642.5112-14.5323-27.5451
40.00310.0081-0.00550.006-0.00460.0113-0.0107-0.0264-0.0011-0.1050.0601-0.0192-0.00890.0090.01630.2004-0.1083-0.016-0.0233-0.02940.126410.0588-7.4539-28.2829
50.0184-0.007-0.0020.0050.00430.0049-0.0068-0.09120.05180.00110.01590.0136-0.1050.023200.0805-0.00140.00860.0635-0.01430.071812.2748-18.587-28.3505
60.00790.0032-0.00860.0141-0.01140.0407-0.0293-0.02140.01180.03580.0143-0.0117-0.1320.038-0.00460.0390.0042-0.00220.0498-0.00440.04140.1828-17.0062-11.6369
70.002-0.00010.00170.0045-0.01030.0109-0.00930.00430.0079-0.0119-0.0073-0.01510.0393-0.0411-00.0423-0.01530.00860.0504-0.00750.0353-8.2255-26.4649-21.2529
80.03610.03420.01670.04090.00630.0291-0.01990.0017-0.0339-0.0202-0.08060.06560.059-0.0318-0.0389-0.0129-0.1758-0.1277-0.0893-0.197-0.1327-9.6879-32.9721-12.7818
90.1659-0.0209-0.03430.1339-0.01270.01650.0557-0.0234-0.0183-0.03030.03670.03020.0758-0.02610.02760.0336-0.0052-0.00410.08190.00290.0149-2.5762-25.2121-5.2899
100.03480.0039-0.00910.03110.010.0317-0.0521-0.0344-0.0772-0.0211-0.03870.0083-0.0062-0.0153-0.05280.00620.08110.083-0.0339-0.08-0.037911.9528-31.5816-38.1399
110.02420.01570.03470.05090.05550.0671-0.0398-0.0414-0.01470.02650.1079-0.0692-0.03750.04580.03980.02180.02440.00830.0341-0.00970.055123.0075-35.816-34.8701
120.04930.03170.00280.0214-0.00760.01570.17780.0310.0156-0.02220.02020.011-0.02480.04750.01810.0411-0.0120.0060.0592-0.0080.098631.1052-28.3397-34.9807
130.00910.01360.00730.013-0.00120.0032-0.02280.08520.0398-0.10190.0202-0.0548-0.01730.0407-00.0607-0.00910.01880.0561-0.00940.057320.1764-25.2711-37.5392
140.00120.0012-0.00040.00510.0070.00760.0241-0.01280.0116-0.06430.0225-0.0259-0.01030.120800.0593-0.01430.00080.0535-0.01680.043722.7435-33.6442-52.8623
150.0014-0.0008-0.00010.0044-0.00090.00070.0730.0099-0.0014-0.01180.0172-0.04590.02720.0379-00.0820.0202-0.010.05080.00530.064223.1084-47.4618-53.2197
160.00040.00060.00410.00060.00160.00930.0787-0.0986-0.03190.0344-0.0590.03720.0948-0.0337-00.0726-0.0198-0.00640.07810.01070.08812.6815-46.1606-44.2871
170.00480.0023-0.00540.0041-0.00480.00450.0165-0.0856-0.0496-0.0142-0.00820.03340.0337-0.0822-0.00230.0801-0.0258-0.01040.08560.01990.06227.186-48.5065-53.0537
180.1449-0.031-0.05840.02150.04950.15220.165-0.0298-0.0726-0.05390.1263-0.00650.1621-0.06070.19680.0760.001-0.0524-0.0131-0.0761-0.095715.5895-41.6861-60.2842
190.03050.004-0.00790.02930.00210.0453-0.04950.05620.01360.0046-0.09910.0483-0.0385-0.0338-0.01380.06040.00010.01110.0613-0.01360.059411.1349-34.2167-50.0995
200.1111-0.00310.0130.0058-0.01810.0864-0.06310.0305-0.02850.0072-0.0698-0.0890.0286-0.0186-0.00910.0518-0.01740.02970.0064-0.00270.0814.2638-28.4329-15.8878
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 2 through 19 )
2X-RAY DIFFRACTION2chain 'B' and (resid 20 through 25 )
3X-RAY DIFFRACTION3chain 'B' and (resid 26 through 44 )
4X-RAY DIFFRACTION4chain 'B' and (resid 45 through 61 )
5X-RAY DIFFRACTION5chain 'B' and (resid 62 through 78 )
6X-RAY DIFFRACTION6chain 'B' and (resid 79 through 101 )
7X-RAY DIFFRACTION7chain 'B' and (resid 102 through 117 )
8X-RAY DIFFRACTION8chain 'B' and (resid 118 through 128 )
9X-RAY DIFFRACTION9chain 'B' and (resid 129 through 147 )
10X-RAY DIFFRACTION10chain 'A' and (resid 2 through 19 )
11X-RAY DIFFRACTION11chain 'A' and (resid 20 through 44 )
12X-RAY DIFFRACTION12chain 'A' and (resid 45 through 61 )
13X-RAY DIFFRACTION13chain 'A' and (resid 62 through 78 )
14X-RAY DIFFRACTION14chain 'A' and (resid 79 through 92 )
15X-RAY DIFFRACTION15chain 'A' and (resid 93 through 101 )
16X-RAY DIFFRACTION16chain 'A' and (resid 102 through 117 )
17X-RAY DIFFRACTION17chain 'A' and (resid 118 through 128 )
18X-RAY DIFFRACTION18chain 'A' and (resid 129 through 147 )
19X-RAY DIFFRACTION19chain 'C' and (resid 78 through 88 )
20X-RAY DIFFRACTION20chain 'D' and (resid 78 through 88 )

+
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