[English] 日本語
Yorodumi
- PDB-4o3a: Crystal structure of the glua2 ligand-binding domain in complex w... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4o3a
TitleCrystal structure of the glua2 ligand-binding domain in complex with L-aspartate at 1.80 a resolution
ComponentsGlutamate receptor 2
KeywordsMEMBRANE PROTEIN/AGONIST / AMPA RECEPTOR LIGAND-BINDING DOMAIN / MEMBRANE PROTEIN-AGONIST complex
Function / homology
Function and homology information


spine synapse / dendritic spine neck / dendritic spine head / Activation of AMPA receptors / perisynaptic space / AMPA glutamate receptor activity / ligand-gated monoatomic cation channel activity / Trafficking of GluR2-containing AMPA receptors / response to lithium ion / immunoglobulin binding ...spine synapse / dendritic spine neck / dendritic spine head / Activation of AMPA receptors / perisynaptic space / AMPA glutamate receptor activity / ligand-gated monoatomic cation channel activity / Trafficking of GluR2-containing AMPA receptors / response to lithium ion / immunoglobulin binding / AMPA glutamate receptor complex / kainate selective glutamate receptor activity / ionotropic glutamate receptor complex / cellular response to glycine / extracellularly glutamate-gated ion channel activity / asymmetric synapse / regulation of receptor recycling / Unblocking of NMDA receptors, glutamate binding and activation / positive regulation of synaptic transmission / glutamate receptor binding / glutamate-gated receptor activity / regulation of synaptic transmission, glutamatergic / response to fungicide / cytoskeletal protein binding / presynaptic active zone membrane / extracellular ligand-gated monoatomic ion channel activity / dendrite membrane / ionotropic glutamate receptor binding / glutamate-gated calcium ion channel activity / somatodendritic compartment / cellular response to brain-derived neurotrophic factor stimulus / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / dendrite cytoplasm / ionotropic glutamate receptor signaling pathway / SNARE binding / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / dendritic shaft / synaptic transmission, glutamatergic / PDZ domain binding / protein tetramerization / synaptic membrane / modulation of chemical synaptic transmission / establishment of protein localization / postsynaptic density membrane / terminal bouton / Schaffer collateral - CA1 synapse / cerebral cortex development / receptor internalization / synaptic vesicle membrane / synaptic vesicle / signaling receptor activity / presynapse / amyloid-beta binding / presynaptic membrane / growth cone / scaffold protein binding / perikaryon / chemical synaptic transmission / postsynaptic membrane / dendritic spine / postsynaptic density / neuron projection / axon / neuronal cell body / dendrite / synapse / protein-containing complex binding / protein kinase binding / glutamatergic synapse / cell surface / endoplasmic reticulum / protein-containing complex / identical protein binding / membrane / plasma membrane
Similarity search - Function
Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / Ligand-gated ion channel / : / Ionotropic glutamate receptor / Eukaryotic homologues of bacterial periplasmic substrate binding proteins. / Receptor, ligand binding region / Receptor family ligand binding region ...Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / Ligand-gated ion channel / : / Ionotropic glutamate receptor / Eukaryotic homologues of bacterial periplasmic substrate binding proteins. / Receptor, ligand binding region / Receptor family ligand binding region / Periplasmic binding protein-like II / Periplasmic binding protein-like I / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / ASPARTIC ACID / DI(HYDROXYETHYL)ETHER / Glutamate receptor 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsKrintel, C. / Frydenvang, F. / Gajhede, M. / Kastrup, J.S.
Citation
Journal: Febs J. / Year: 2014
Title: L-Asp is a useful tool in the purification of the ionotropic glutamate receptor A2 ligand-binding domain.
Authors: Krintel, C. / Frydenvang, K. / Ceravalls de Rabassa, A. / Kaern, A.M. / Gajhede, M. / Pickering, D.S. / Kastrup, J.S.
#1: Journal: Neuron / Year: 2000
Title: Mechanisms for activation and antagonism of an AMPA-sensitive glutamate receptor: crystal structures of the GluR2 ligand binding core.
Authors: Armstrong, N. / Gouaux, E.
History
DepositionDec 18, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 16, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 18, 2014Group: Database references
Revision 1.2Dec 14, 2016Group: Structure summary
Revision 1.3May 31, 2017Group: Structure summary
Revision 1.4Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.5Sep 20, 2023Group: 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 / 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_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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Glutamate receptor 2
B: Glutamate receptor 2
C: Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,80942
Polymers87,6653
Non-polymers3,14339
Water11,133618
1
A: Glutamate receptor 2
hetero molecules

A: Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,56128
Polymers58,4432
Non-polymers2,11826
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
Buried area5680 Å2
ΔGint-147 kcal/mol
Surface area24000 Å2
MethodPISA
2
B: Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,26713
Polymers29,2221
Non-polymers1,04512
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,26115
Polymers29,2221
Non-polymers1,03914
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)114.661, 162.211, 47.346
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

-
Components

-
Protein , 1 types, 3 molecules ABC

#1: Protein Glutamate receptor 2 / GluR-2 / AMPA-selective glutamate receptor 2 / GluR-B / GluR-K2 / Glutamate receptor ionotropic / AMPA 2


Mass: 29221.682 Da / Num. of mol.: 3
Fragment: Ligand binding domain (unp residues 413-527 and unp residues 653-736)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Gria2, Glur2 / Plasmid: pET-22b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): Origami B (DE3) / References: UniProt: P19491

-
Non-polymers , 7 types, 657 molecules

#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-ASP / ASPARTIC ACID


Type: L-peptide linking / Mass: 133.103 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H7NO4
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Zn
#5: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 618 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.51 Å3/Da / Density % sol: 51.02 %
Crystal growTemperature: 279 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 24.4 % PEG 4000, 0.1 M zinc acetate and 0.1 M sodium acetate., pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 279K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: May 14, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→29.252 Å / Num. all: 81356 / Num. obs: 81356 / % possible obs: 98.3 % / Redundancy: 5.9 % / Biso Wilson estimate: 18.6 Å2 / Rsym value: 0.079 / Net I/σ(I): 12.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.8-1.95.70.4241.868282118890.42499.5
1.9-2.015.80.2612.965376112390.26199.6
2.01-2.155.80.1624.661630105440.16299
2.15-2.325.90.1235.75785298450.12399.3
2.32-2.555.90.1016.85338190360.10198.5
2.55-2.855.90.0827.84832881520.08298.1
2.85-3.295.90.0698.44272271860.06997.6
3.29-4.0260.069.53630460850.0696.5
4.02-5.695.90.0559.72815247360.05595.8
5.69-29.2525.70.05210.31499526440.05292.6

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.8 Å29.25 Å
Translation4.82 Å29.25 Å

-
Processing

Software
NameVersionClassificationNB
SCALA3.3.21data scaling
PHASER2.5.2phasing
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1M5B

1m5b


Resolution: 1.8→29.252 Å / Occupancy max: 1 / Occupancy min: 0.25 / SU ML: 0.17 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0.28 / Phase error: 18.13 / Stereochemistry target values: ML
Details: refinement done with TLS, isotropic B-factors and riding hydrogens
RfactorNum. reflection% reflectionSelection details
Rfree0.1881 4056 4.99 %RANDOM
Rwork0.1532 ---
obs0.1549 77227 98.34 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 110.02 Å2 / Biso mean: 25.5309 Å2 / Biso min: 8.83 Å2
Refinement stepCycle: LAST / Resolution: 1.8→29.252 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6120 0 177 618 6915
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0116475
X-RAY DIFFRACTIONf_angle_d1.2988684
X-RAY DIFFRACTIONf_chiral_restr0.076951
X-RAY DIFFRACTIONf_plane_restr0.0061091
X-RAY DIFFRACTIONf_dihedral_angle_d13.9342468
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection allNum. reflection obs% reflection obs (%)
1.8-1.82050.27952810.236949885269498899
1.8205-1.84190.28842420.2223497252144972100
1.8419-1.86430.20852430.1979501452575014100
1.8643-1.88790.24462710.1974501152825011100
1.8879-1.91280.22872340.199849645198496499
1.9128-1.9390.25922600.195502352835023100
1.939-1.96670.24622510.186850235274502399
1.9667-1.9960.23072680.183648555123485599
1.996-2.02720.22072600.1663505553155055100
2.0272-2.06040.20362490.160749715220497198
2.0604-2.09590.18622630.1585495252154952100
2.0959-2.1340.21272780.156349705248497099
2.134-2.17510.20382410.153449785219497898
2.1751-2.21940.20542590.1543496552244965100
2.2194-2.26770.19592590.146249205179492098
2.2677-2.32040.21332520.1533496852204968100
2.3204-2.37840.18982830.150348905173489098
2.3784-2.44270.17412430.1484499052334990100
2.4427-2.51450.19252550.143849425197494298
2.5145-2.59560.16882580.141549255183492599
2.5956-2.68840.17182900.137348725162487298
2.6884-2.79590.19592800.151148855165488597
2.7959-2.92310.18372360.148949085144490899
2.9231-3.0770.18032900.145148515141485198
3.077-3.26960.17742810.14648465127484697
3.2696-3.52160.15562950.14348045099480497
3.5216-3.87530.15252330.134448705103487096
3.8753-4.43440.16072580.127747995057479996
4.4344-5.58050.17842240.136247875011478796
5.5805-29.25580.20642290.186747144943471493
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)
11.9504-0.28060.62752.113-0.19151.8089-0.03240.11710.1445-0.0522-0.0115-0.1272-0.12530.20140.01330.0942-0.02490.00990.13730.00550.0951-39.490110.4733-12.8686
20.3728-0.21340.08831.00251.02413.1328-0.03110.0343-0.01070.0396-0.05230.0722-0.01160.03690.09620.0721-0.01420.00120.0950.00560.1018-52.763710.7187-6.3534
32.7173-0.57220.17023.3940.21692.0535-0.03590.12770.24950.013-0.05380.155-0.1794-0.02770.07270.125-0.0124-0.00220.10070.01690.1118-54.640519.59174.7332
42.0819-0.07740.4473.12550.57842.68910.0058-0.1578-0.21350.04660.0310.01890.10160.0933-0.0360.0551-0.00220.01360.13020.00970.1117-45.9337-0.4355-7.2501
52.59980.19270.08482.7337-0.10812.32930.0221-0.0186-0.1028-0.04170.0072-0.21690.17680.2383-0.00940.13070.0350.00740.120.00360.1496-37.773339.8363-2.4657
61.24970.47830.42220.8040.55423.295-0.0460.0060.1206-0.08730.0154-0.0079-0.2080.24710.02740.1236-0.00240.01640.10140.00170.1918-39.351655.95620.1798
72.74831.00970.6013.7968-1.34172.3026-0.01-0.20610.25190.0436-0.2026-0.1349-0.12880.17110.18420.1291-0.01450.0250.1957-0.0440.1824-33.99660.825614.0259
83.37940.1709-0.91730.94620.36794.5366-0.10720.2098-0.0528-0.15470.09920.11360.07-0.11830.01980.1450.0154-0.0120.07910.02360.186-50.75848.1748-5.787
94.51410.89373.28323.32670.67882.51380.3643-0.8336-0.14780.4032-0.26810.14940.3758-0.6281-0.01070.2128-0.0330.03780.23810.04070.1938-47.350640.605113.2385
101.8908-0.30830.41912.37170.94522.06370.0582-0.1579-0.18590.0862-0.00590.04710.1369-0.1326-0.03620.1048-0.0372-0.00180.12820.04370.1414-12.384814.60183.4258
111.7851-0.1815-0.03970.5984-0.14532.6710.08960.14940.0914-0.10230.0319-0.0429-0.3628-0.1701-0.09310.2308-0.02850.03820.1045-0.00120.183-9.88926.4443-10.2888
120.7-0.50730.46271.38950.34630.71050.0615-0.07250.24970.1375-0.0684-0.0843-0.1516-0.0970.0840.16090.00320.08690.09530.01180.0124-34.645838.0256-0.6259
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1:79 )A1 - 79
2X-RAY DIFFRACTION2( CHAIN A AND RESID 80:123 )A80 - 123
3X-RAY DIFFRACTION3( CHAIN A AND RESID 124:217 )A124 - 217
4X-RAY DIFFRACTION4( CHAIN A AND RESID 218:261 )A218 - 261
5X-RAY DIFFRACTION5( CHAIN B AND RESID 1:65 )B1 - 65
6X-RAY DIFFRACTION6( CHAIN B AND RESID 66:123 )B66 - 123
7X-RAY DIFFRACTION7( CHAIN B AND RESID 124:217 )B124 - 217
8X-RAY DIFFRACTION8( CHAIN B AND RESID 218:243 )B218 - 243
9X-RAY DIFFRACTION9( CHAIN B AND RESID 244:263 )B244 - 263
10X-RAY DIFFRACTION10( CHAIN C AND RESID 1:93 )C1 - 93
11X-RAY DIFFRACTION11( CHAIN C AND RESID 94:262 )C94 - 262
12X-RAY DIFFRACTION12( CHAIN A AND RESID 302:302 ) OR ( CHAIN C AND RESID 301:301 ) OR ( CHAIN B AND RESID 301:301 )A302
13X-RAY DIFFRACTION12( CHAIN A AND RESID 302:302 ) OR ( CHAIN C AND RESID 301:301 ) OR ( CHAIN B AND RESID 301:301 )C301
14X-RAY DIFFRACTION12( CHAIN A AND RESID 302:302 ) OR ( CHAIN C AND RESID 301:301 ) OR ( CHAIN B AND RESID 301:301 )B301

+
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