[English] 日本語
Yorodumi
- PDB-5how: X-ray crystallographic structure of an Abeta 17-36 beta-hairpin. ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5how
TitleX-ray crystallographic structure of an Abeta 17-36 beta-hairpin. LV(PHI)FAEDCGSNKCAII(SAR)L(ORN)V
ComponentsAmyloid beta A4 protein
KeywordsPROTEIN FIBRIL / amyloid / oligomer / beta-hairpin / Alzheimer's
Function / homology
Function and homology information


amyloid-beta complex / negative regulation of presynapse assembly / cytosolic mRNA polyadenylation / collateral sprouting in absence of injury / microglia development / regulation of synapse structure or activity / regulation of Wnt signaling pathway / synaptic assembly at neuromuscular junction / Formyl peptide receptors bind formyl peptides and many other ligands / axo-dendritic transport ...amyloid-beta complex / negative regulation of presynapse assembly / cytosolic mRNA polyadenylation / collateral sprouting in absence of injury / microglia development / regulation of synapse structure or activity / regulation of Wnt signaling pathway / synaptic assembly at neuromuscular junction / Formyl peptide receptors bind formyl peptides and many other ligands / axo-dendritic transport / axon midline choice point recognition / smooth endoplasmic reticulum calcium ion homeostasis / astrocyte activation involved in immune response / NMDA selective glutamate receptor signaling pathway / mating behavior / regulation of spontaneous synaptic transmission / ciliary rootlet / Golgi-associated vesicle / PTB domain binding / Lysosome Vesicle Biogenesis / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / positive regulation of amyloid fibril formation / neuron remodeling / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / nuclear envelope lumen / COPII-coated ER to Golgi transport vesicle / suckling behavior / signaling receptor activator activity / dendrite development / modulation of excitatory postsynaptic potential / TRAF6 mediated NF-kB activation / presynaptic active zone / positive regulation of protein metabolic process / neuromuscular process controlling balance / Advanced glycosylation endproduct receptor signaling / The NLRP3 inflammasome / negative regulation of long-term synaptic potentiation / regulation of presynapse assembly / regulation of multicellular organism growth / transition metal ion binding / intracellular copper ion homeostasis / negative regulation of neuron differentiation / ECM proteoglycans / spindle midzone / positive regulation of T cell migration / smooth endoplasmic reticulum / Purinergic signaling in leishmaniasis infection / forebrain development / positive regulation of chemokine production / clathrin-coated pit / Notch signaling pathway / protein serine/threonine kinase binding / positive regulation of G2/M transition of mitotic cell cycle / extracellular matrix organization / neuron projection maintenance / Mitochondrial protein degradation / response to interleukin-1 / ionotropic glutamate receptor signaling pathway / positive regulation of mitotic cell cycle / cholesterol metabolic process / axonogenesis / positive regulation of calcium-mediated signaling / dendritic shaft / platelet alpha granule lumen / adult locomotory behavior / positive regulation of glycolytic process / central nervous system development / learning / positive regulation of interleukin-1 beta production / trans-Golgi network membrane / positive regulation of long-term synaptic potentiation / endosome lumen / locomotory behavior / astrocyte activation / Post-translational protein phosphorylation / positive regulation of JNK cascade / microglial cell activation / regulation of long-term neuronal synaptic plasticity / serine-type endopeptidase inhibitor activity / synapse organization / TAK1-dependent IKK and NF-kappa-B activation / positive regulation of non-canonical NF-kappaB signal transduction / neuromuscular junction / visual learning / recycling endosome / positive regulation of interleukin-6 production / Golgi lumen / cognition / neuron cellular homeostasis / positive regulation of inflammatory response / endocytosis / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / cellular response to amyloid-beta / neuron projection development / G2/M transition of mitotic cell cycle / positive regulation of tumor necrosis factor production / apical part of cell / synaptic vesicle / cell-cell junction / Platelet degranulation
Similarity search - Function
Amyloidogenic glycoprotein, copper-binding / Amyloidogenic glycoprotein, copper-binding domain conserved site / Amyloidogenic glycoprotein, copper-binding domain superfamily / Copper-binding of amyloid precursor, CuBD / Amyloid precursor protein (APP) copper-binding (CuBD) domain signature. / Amyloidogenic glycoprotein, amyloid-beta peptide superfamily / Beta-amyloid peptide (beta-APP) / Amyloidogenic glycoprotein, amyloid-beta peptide / Beta-amyloid precursor protein C-terminal / Amyloidogenic glycoprotein, intracellular domain, conserved site ...Amyloidogenic glycoprotein, copper-binding / Amyloidogenic glycoprotein, copper-binding domain conserved site / Amyloidogenic glycoprotein, copper-binding domain superfamily / Copper-binding of amyloid precursor, CuBD / Amyloid precursor protein (APP) copper-binding (CuBD) domain signature. / Amyloidogenic glycoprotein, amyloid-beta peptide superfamily / Beta-amyloid peptide (beta-APP) / Amyloidogenic glycoprotein, amyloid-beta peptide / Beta-amyloid precursor protein C-terminal / Amyloidogenic glycoprotein, intracellular domain, conserved site / Beta-amyloid precursor protein C-terminus / Amyloid precursor protein (APP) intracellular domain signature. / Amyloidogenic glycoprotein, extracellular / Amyloidogenic glycoprotein, heparin-binding / Amyloidogenic glycoprotein, E2 domain / E2 domain superfamily / Amyloidogenic glycoprotein, heparin-binding domain superfamily / Amyloid A4 N-terminal heparin-binding / E2 domain of amyloid precursor protein / Amyloid precursor protein (APP) E1 domain profile. / Amyloid precursor protein (APP) E2 domain profile. / amyloid A4 / Amyloidogenic glycoprotein / Proteinase inhibitor I2, Kunitz, conserved site / Pancreatic trypsin inhibitor (Kunitz) family signature. / BPTI/Kunitz family of serine protease inhibitors. / Pancreatic trypsin inhibitor Kunitz domain / Kunitz/Bovine pancreatic trypsin inhibitor domain / Pancreatic trypsin inhibitor (Kunitz) family profile. / Pancreatic trypsin inhibitor Kunitz domain superfamily / PH-like domain superfamily
Similarity search - Domain/homology
Amyloid-beta precursor protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.295 Å
AuthorsKreutzer, A.G. / Nowick, J.S. / Spencer, R.K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM097562 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2016
Title: X-ray Crystallographic Structures of a Trimer, Dodecamer, and Annular Pore Formed by an A beta 17-36 beta-Hairpin.
Authors: Kreutzer, A.G. / Hamza, I.L. / Spencer, R.K. / Nowick, J.S.
History
DepositionJan 19, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 20, 2016Group: Database references
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Apr 2, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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_label_atom_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Amyloid beta A4 protein
B: Amyloid beta A4 protein
C: Amyloid beta A4 protein
D: Amyloid beta A4 protein
E: Amyloid beta A4 protein
F: Amyloid beta A4 protein


Theoretical massNumber of molelcules
Total (without water)14,2116
Polymers14,2116
Non-polymers00
Water66737
1
A: Amyloid beta A4 protein
B: Amyloid beta A4 protein
C: Amyloid beta A4 protein
D: Amyloid beta A4 protein
E: Amyloid beta A4 protein
F: Amyloid beta A4 protein

A: Amyloid beta A4 protein
B: Amyloid beta A4 protein
C: Amyloid beta A4 protein
D: Amyloid beta A4 protein
E: Amyloid beta A4 protein
F: Amyloid beta A4 protein


Theoretical massNumber of molelcules
Total (without water)28,42312
Polymers28,42312
Non-polymers00
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_556x,x-y,-z+7/61
Buried area11330 Å2
ΔGint-79 kcal/mol
Surface area13490 Å2
MethodPISA
2
A: Amyloid beta A4 protein
B: Amyloid beta A4 protein
E: Amyloid beta A4 protein


Theoretical massNumber of molelcules
Total (without water)7,1063
Polymers7,1063
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1500 Å2
ΔGint-11 kcal/mol
Surface area4730 Å2
MethodPISA
3
A: Amyloid beta A4 protein
B: Amyloid beta A4 protein
E: Amyloid beta A4 protein

A: Amyloid beta A4 protein
B: Amyloid beta A4 protein
E: Amyloid beta A4 protein


Theoretical massNumber of molelcules
Total (without water)14,2116
Polymers14,2116
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+4/31
Buried area3930 Å2
ΔGint-28 kcal/mol
Surface area8540 Å2
MethodPISA
4
C: Amyloid beta A4 protein
D: Amyloid beta A4 protein
F: Amyloid beta A4 protein


Theoretical massNumber of molelcules
Total (without water)7,1063
Polymers7,1063
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1490 Å2
ΔGint-11 kcal/mol
Surface area4690 Å2
MethodPISA
5
C: Amyloid beta A4 protein
D: Amyloid beta A4 protein
F: Amyloid beta A4 protein

C: Amyloid beta A4 protein
D: Amyloid beta A4 protein
F: Amyloid beta A4 protein


Theoretical massNumber of molelcules
Total (without water)14,2116
Polymers14,2116
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_656-x+y+1,y,-z+3/21
Buried area4690 Å2
ΔGint-37 kcal/mol
Surface area7670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.310, 97.310, 97.621
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-104-

HOH

-
Components

#1: Protein/peptide
Amyloid beta A4 protein / ABPP / APPI / APP / Alzheimer disease amyloid protein / Cerebral vascular amyloid peptide / CVAP / ...ABPP / APPI / APP / Alzheimer disease amyloid protein / Cerebral vascular amyloid peptide / CVAP / PreA4 / Protease nexin-II / PN-II


Mass: 2368.577 Da / Num. of mol.: 6 / Fragment: UNP residues 687-707 / Mutation: F19PHI, V24C, G29C, G33Sar, M35Orn / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P05067*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.71 Å3/Da / Density % sol: 73.9 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 6.4 / Details: 0.1 M HEPES Buffer, 31% (v/v) Jeffamine M-600 / PH range: 6.5-7.5 / Temp details: Room temperature

-
Data collection

DiffractionMean temperature: 133 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 92 / Detector: CCD / Date: Jul 15, 2015
RadiationMonochromator: Cu / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.295→28.09 Å / Num. obs: 12701 / % possible obs: 100 % / Redundancy: 2 % / CC1/2: 0.994 / Rmerge(I) obs: 0.05629 / Net I/σ(I): 15.73
Reflection shellResolution: 2.295→2.377 Å / Redundancy: 2 % / Rmerge(I) obs: 0.4378 / Mean I/σ(I) obs: 1.41 / % possible all: 99

-
Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
Aimless0.5.17data scaling
PHASER1.10.1_2155phasing
RefinementResolution: 2.295→28.091 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2622 1270 9.86 %Random selection
Rwork0.2335 ---
obs0.2365 12695 99.92 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.295→28.091 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms936 0 0 37 973
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005954
X-RAY DIFFRACTIONf_angle_d0.9341278
X-RAY DIFFRACTIONf_dihedral_angle_d20.214606
X-RAY DIFFRACTIONf_chiral_restr0.046150
X-RAY DIFFRACTIONf_plane_restr0.004162
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.295-2.34490.39061440.37941280X-RAY DIFFRACTION99
2.3449-2.39940.42121380.35221285X-RAY DIFFRACTION100
2.3994-2.45940.36531470.3421308X-RAY DIFFRACTION100
2.4594-2.52580.36041460.34471305X-RAY DIFFRACTION100
2.5258-2.60010.40081440.33181314X-RAY DIFFRACTION100
2.6001-2.6840.38581410.33551281X-RAY DIFFRACTION100
2.684-2.77980.33971390.29621312X-RAY DIFFRACTION100
2.7798-2.8910.29931370.28461299X-RAY DIFFRACTION100
2.891-3.02240.34251430.27581315X-RAY DIFFRACTION100
3.0224-3.18160.3261440.24141297X-RAY DIFFRACTION100
3.1816-3.38060.27471440.25811303X-RAY DIFFRACTION100
3.3806-3.64110.23181400.2361294X-RAY DIFFRACTION100
3.6411-4.00660.22781440.21321301X-RAY DIFFRACTION100
4.0066-4.58420.19591410.16751307X-RAY DIFFRACTION100
4.5842-5.76740.19741400.18171318X-RAY DIFFRACTION100
5.7674-28.0930.23521450.20211302X-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)
14.7812.08184.3053.74175.08968.1116-0.5936-0.57230.5292-0.6310.28230.2275-1.0806-0.05970.39710.432-0.06870.04030.7644-0.0410.559522.288420.738763.1979
24.59782.0637-0.77574.0808-4.50895.62270.1614-0.5592-1.539-1.4863-1.06122.7846-0.7273-1.45631.24491.1852-0.2681-0.30051.81760.01631.196510.863211.119255.9003
33.02233.06891.14098.1614.95483.258-0.5022-1.5709-1.4883-0.71250.15380.19480.0961-1.18970.30840.47650.03670.05940.8270.07170.679922.480418.734566.4217
44.27133.49872.50443.681.52818.4540.52740.6671-0.7372-0.4346-0.68080.15360.2439-0.33160.33750.40930.10760.09190.71710.06850.632721.79125.33756.2899
56.2479-7.356-2.62489.33841.15556.5658-0.6786-0.5493.4669-1.1130.0748-3.025-2.66730.14381.31661.14880.2038-0.08980.88850.24561.275922.784541.439252.2239
63.1687-1.9671.78352.33460.24352.37580.61710.5602-0.1104-0.3651-0.92150.1302-0.1003-0.0050.18010.52560.14750.02650.7171-0.01970.608420.150723.944553.2207
73.3734-2.1213-0.53556.5019-3.66433.7561.45790.7702-0.4869-0.5829-1.365-0.37571.3397-1.67020.28250.63350.0673-0.06560.7274-0.06330.411440.206819.262470.093
82.09351.9336-1.84171.7546-1.64971.5772-0.3469-5.45070.7571.76612.9235-0.7032-1.2283-0.86063.26011.32740.64390.68821.70920.07981.262733.210529.562480.5247
92.82242.81283.64767.59788.09189.51760.2031-1.01540.67462.47070.8506-0.36512.44140.0442-1.16040.6238-0.0330.06050.6616-0.10750.540938.308121.117875.5853
104.6327-0.54633.12683.7256-2.22673.0875-1.07370.96790.44571.7195-0.073-1.8392.4001-0.4488-0.7420.7686-0.0754-0.15120.5374-0.07230.537639.17019.756265.6896
114.49120.16340.494.44535.13795.97240.87411.0454-0.41110.7537-1.6562-0.60011.51061.7420.38670.68670.0621-0.16880.5415-0.0290.665746.764411.735966.5719
127.47885.5691-2.52214.6317-2.8954.1571-0.07210.36660.1207-0.03-0.3137-1.12640.40730.65640.33290.551-0.0084-0.05630.61390.03770.526749.259616.687162.3261
139.3543-2.0994-1.1324.6889-1.80217.90510.14-0.19850.3371-0.07310.7684-0.35020.744-0.4856-0.9420.59070.22480.01690.6478-0.08740.542425.785927.666469.2083
144.3669-0.8835-0.41488.1475-4.45793.7292-0.4961-0.01720.0571-0.12030.1142-0.88580.0884-0.35340.16110.58910.02740.02420.5046-0.04440.50427.113931.83763.0438
158.0323-0.5842-7.88287.4467-0.18848.7510.1060.8880.64790.37120.0152-0.252-0.19480.03250.34340.4411-0.1466-0.10420.7897-0.12150.516344.404825.283366.2753
165.48190.2964.90921.27880.65158.2108-3.7931-0.08791.4279-1.55184.101-1.99660.1141-0.3549-0.47711.4879-0.15060.5691.4369-0.56861.894558.531629.186958.8153
172.341.67620.19473.3557-2.96774.344-0.1618-0.04041.5613-0.24-0.13710.5272-0.4746-0.16110.51780.5450.0017-0.03720.446-0.07030.678743.304128.760466.9214
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 6 )
2X-RAY DIFFRACTION2chain 'A' and (resid 7 through 11 )
3X-RAY DIFFRACTION3chain 'A' and (resid 12 through 21 )
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 6 )
5X-RAY DIFFRACTION5chain 'B' and (resid 7 through 11 )
6X-RAY DIFFRACTION6chain 'B' and (resid 12 through 21 )
7X-RAY DIFFRACTION7chain 'C' and (resid 1 through 6 )
8X-RAY DIFFRACTION8chain 'C' and (resid 7 through 11 )
9X-RAY DIFFRACTION9chain 'C' and (resid 12 through 17 )
10X-RAY DIFFRACTION10chain 'C' and (resid 19 through 21 )
11X-RAY DIFFRACTION11chain 'D' and (resid 1 through 11 )
12X-RAY DIFFRACTION12chain 'D' and (resid 12 through 21 )
13X-RAY DIFFRACTION13chain 'E' and (resid 1 through 11 )
14X-RAY DIFFRACTION14chain 'E' and (resid 12 through 21 )
15X-RAY DIFFRACTION15chain 'F' and (resid 1 through 6 )
16X-RAY DIFFRACTION16chain 'F' and (resid 7 through 11 )
17X-RAY DIFFRACTION17chain 'F' and (resid 12 through 21 )

+
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