[English] 日本語
Yorodumi
- PDB-4cc7: Crystal structure of the sixth or C-terminal SH3 domain of human ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4cc7
TitleCrystal structure of the sixth or C-terminal SH3 domain of human Tuba in complex with proline-rich peptides of N-WASP. Space group P41
Components
  • DYNAMIN-BINDING PROTEIN
  • NEURAL WISKOTT-ALDRICH SYNDROME PROTEIN
KeywordsSTRUCTURAL PROTEIN / SRC HOMOLOGY 3 / PROLINE-RICH PEPTIDE / ACTIN CYTOSKELETON / CORTICAL TENSION / CELL-CELL CONTACTS
Function / homology
Function and homology information


negative regulation of membrane tubulation / spindle localization / positive regulation of clathrin-dependent endocytosis / negative regulation of lymphocyte migration / NOSTRIN mediated eNOS trafficking / GTPase regulator activity / actin cap / vesicle organization / vesicle transport along actin filament / vesicle budding from membrane ...negative regulation of membrane tubulation / spindle localization / positive regulation of clathrin-dependent endocytosis / negative regulation of lymphocyte migration / NOSTRIN mediated eNOS trafficking / GTPase regulator activity / actin cap / vesicle organization / vesicle transport along actin filament / vesicle budding from membrane / Golgi stack / actin polymerization or depolymerization / dendritic spine morphogenesis / protein-containing complex localization / Nephrin family interactions / DCC mediated attractive signaling / regulation of small GTPase mediated signal transduction / positive regulation of filopodium assembly / regulation of postsynapse organization / RHOV GTPase cycle / RHOJ GTPase cycle / RHOQ GTPase cycle / CDC42 GTPase cycle / cilium assembly / RHO GTPases Activate WASPs and WAVEs / EPHB-mediated forward signaling / RAC1 GTPase cycle / actin filament polymerization / guanyl-nucleotide exchange factor activity / FCGR3A-mediated phagocytosis / response to bacterium / Regulation of actin dynamics for phagocytic cup formation / endocytic vesicle membrane / cell-cell junction / actin cytoskeleton / lamellipodium / regulation of protein localization / presynapse / Clathrin-mediated endocytosis / regulation of cell shape / actin binding / protein-containing complex assembly / cytoplasmic vesicle / microtubule binding / cytoskeleton / intracellular signal transduction / cell division / glutamatergic synapse / synapse / endoplasmic reticulum membrane / Golgi apparatus / positive regulation of transcription by RNA polymerase II / extracellular exosome / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Dynamin-binding protein, first N-terminal SH3 domain / Dynamin-binding protein, second N-terminal SH3 domain / Dynamin-binding protein, third N-terminal SH3 domain / Dynamin-binding protein, first C-terminal SH3 domain / : / Actin nucleation-promoting factor WAS, C-terminal / WASP family, EVH1 domain / Wiskott Aldrich syndrome homology region 2 / BAR domain / BAR domain profile. ...Dynamin-binding protein, first N-terminal SH3 domain / Dynamin-binding protein, second N-terminal SH3 domain / Dynamin-binding protein, third N-terminal SH3 domain / Dynamin-binding protein, first C-terminal SH3 domain / : / Actin nucleation-promoting factor WAS, C-terminal / WASP family, EVH1 domain / Wiskott Aldrich syndrome homology region 2 / BAR domain / BAR domain profile. / BAR / WH2 motif / WH1/EVH1 domain / WH1 domain / WH1 domain profile. / WASP homology region 1 / WH2 domain / WH2 domain profile. / BAR domain / CRIB domain superfamily / P21-Rho-binding domain / CRIB domain profile. / P21-Rho-binding domain / CRIB domain / Guanine-nucleotide dissociation stimulator, CDC24, conserved site / Dbl homology (DH) domain signature. / AH/BAR domain superfamily / Variant SH3 domain / Variant SH3 domain / Dbl homology (DH) domain superfamily / RhoGEF domain / Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases / Dbl homology (DH) domain / Dbl homology (DH) domain profile. / SH3 Domains / SH3 domain / SH3 type barrels. / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / PH-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
Actin nucleation-promoting factor WASL / Dynamin-binding protein
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsPolle, L. / Rigano, L. / Julian, R. / Ireton, K. / Schubert, W.-D.
CitationJournal: Structure / Year: 2014
Title: Structural Details of Human Tuba Recruitment by Inlc of Listeria Monocytogenes Elucidate Bacterial Cell-Cell Spreading.
Authors: Polle, L. / Rigano, L.A. / Julian, R. / Ireton, K. / Schubert, W.
History
DepositionOct 18, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 30, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2014Group: Database references
Revision 1.2Feb 19, 2014Group: Database references
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.status_code_sf / _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_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_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_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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DYNAMIN-BINDING PROTEIN
B: NEURAL WISKOTT-ALDRICH SYNDROME PROTEIN
C: DYNAMIN-BINDING PROTEIN
D: NEURAL WISKOTT-ALDRICH SYNDROME PROTEIN
E: DYNAMIN-BINDING PROTEIN
F: NEURAL WISKOTT-ALDRICH SYNDROME PROTEIN
G: DYNAMIN-BINDING PROTEIN
H: NEURAL WISKOTT-ALDRICH SYNDROME PROTEIN
I: DYNAMIN-BINDING PROTEIN
J: NEURAL WISKOTT-ALDRICH SYNDROME PROTEIN
K: DYNAMIN-BINDING PROTEIN
L: NEURAL WISKOTT-ALDRICH SYNDROME PROTEIN
M: DYNAMIN-BINDING PROTEIN
N: NEURAL WISKOTT-ALDRICH SYNDROME PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,54837
Polymers61,52914
Non-polymers1,02023
Water3,981221
1
A: DYNAMIN-BINDING PROTEIN
B: NEURAL WISKOTT-ALDRICH SYNDROME PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,9535
Polymers8,7902
Non-polymers1633
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1260 Å2
ΔGint-21.2 kcal/mol
Surface area4210 Å2
MethodPISA
2
C: DYNAMIN-BINDING PROTEIN
D: NEURAL WISKOTT-ALDRICH SYNDROME PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,9886
Polymers8,7902
Non-polymers1984
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1900 Å2
ΔGint-34.7 kcal/mol
Surface area4640 Å2
MethodPISA
3
E: DYNAMIN-BINDING PROTEIN
F: NEURAL WISKOTT-ALDRICH SYNDROME PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,8614
Polymers8,7902
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1280 Å2
ΔGint-23.5 kcal/mol
Surface area4580 Å2
MethodPISA
4
G: DYNAMIN-BINDING PROTEIN
H: NEURAL WISKOTT-ALDRICH SYNDROME PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,8614
Polymers8,7902
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1400 Å2
ΔGint-21.7 kcal/mol
Surface area4430 Å2
MethodPISA
5
I: DYNAMIN-BINDING PROTEIN
J: NEURAL WISKOTT-ALDRICH SYNDROME PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,8253
Polymers8,7902
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1200 Å2
ΔGint-13.1 kcal/mol
Surface area4480 Å2
MethodPISA
6
K: DYNAMIN-BINDING PROTEIN
L: NEURAL WISKOTT-ALDRICH SYNDROME PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,0137
Polymers8,7902
Non-polymers2235
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1760 Å2
ΔGint-38.3 kcal/mol
Surface area4190 Å2
MethodPISA
7
M: DYNAMIN-BINDING PROTEIN
N: NEURAL WISKOTT-ALDRICH SYNDROME PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,0488
Polymers8,7902
Non-polymers2586
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1940 Å2
ΔGint-46.9 kcal/mol
Surface area4210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.570, 88.570, 69.730
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

-
Components

-
Protein / Protein/peptide , 2 types, 14 molecules ACEGIKMBDFHJLN

#1: Protein
DYNAMIN-BINDING PROTEIN / SCAFFOLD PROTEIN TUBA


Mass: 7712.617 Da / Num. of mol.: 7 / Fragment: C-TERMINAL SH3 DOMAIN OF TUBA, RESIDUES 1513-1577
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): CODONPLUS / References: UniProt: Q6XZF7
#2: Protein/peptide
NEURAL WISKOTT-ALDRICH SYNDROME PROTEIN / N-WASP / N-WASP


Mass: 1077.188 Da / Num. of mol.: 7 / Fragment: PROLINE-RICH REGION, RESIDUES 346-357 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: O00401

-
Non-polymers , 4 types, 244 molecules

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


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 221 / Source method: isolated from a natural source / Formula: H2O

-
Details

Sequence detailsTHE TWO N-TERMINAL RESIDUES GP ARE REMNANTS OF THE FUSION PROTEIN CLEAVAGE SITE.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.17 Å3/Da / Density % sol: 43.37 % / Description: NONE
Crystal growpH: 5.5 / Details: 3 M NACL, 0.1 M BIS-TRIS PH 5.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 18, 2011 / Details: KIRKPATRICK-BAEZ PAIR OF BI-MORPH MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.97→50 Å / Num. obs: 38387 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 6 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 20.7
Reflection shellResolution: 1.97→2.09 Å / Redundancy: 6 % / Rmerge(I) obs: 0.71 / Mean I/σ(I) obs: 2.6 / % possible all: 99.2

-
Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ZUU

1zuu


Resolution: 1.97→46.59 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.945 / SU B: 7.047 / SU ML: 0.101 / Cross valid method: THROUGHOUT / ESU R: 0.171 / ESU R Free: 0.149 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED.
RfactorNum. reflection% reflectionSelection details
Rfree0.21459 1920 5 %RANDOM
Rwork0.1761 ---
obs0.17798 36465 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 42.248 Å2
Baniso -1Baniso -2Baniso -3
1--0.82 Å20 Å20 Å2
2---0.82 Å20 Å2
3---1.64 Å2
Refinement stepCycle: LAST / Resolution: 1.97→46.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4000 0 43 221 4264
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.024295
X-RAY DIFFRACTIONr_bond_other_d0.0130.024197
X-RAY DIFFRACTIONr_angle_refined_deg2.0381.9615834
X-RAY DIFFRACTIONr_angle_other_deg2.18239719
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7845505
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.37224.815189
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.95915747
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8451516
X-RAY DIFFRACTIONr_chiral_restr0.1320.2629
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0214728
X-RAY DIFFRACTIONr_gen_planes_other0.0130.02968
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.966→2.017 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 140 -
Rwork0.236 2645 -
obs--97.96 %
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)
17.5466-2.862-1.27676.21210.61926.28910.21710.8321-0.0736-0.603-0.3507-0.1931-0.1569-0.23910.13360.28820.0380.02690.3005-0.01930.091340.671-70.017-23.054
25.62940.55270.52554.13950.58332.0594-0.029-0.1299-0.42610.06750.03320.19060.0687-0.0847-0.00420.1905-0.0006-0.00240.23960.01310.082222.566-62.19-12.536
34.15860.20880.25363.6051-0.86215.2622-0.1187-0.27070.20520.10750.14550.2277-0.2502-0.3221-0.02680.19790.0133-0.01290.2611-0.00380.15725.863-51.46-21.761
47.35040.74640.61654.56680.58013.7869-0.20260.2283-0.0154-0.18110.05760.1346-0.0475-0.11980.1450.2293-0.0119-0.02190.2890.02510.1477-9.58-60.735-34.523
55.9132.4598-1.60214.2393-2.47696.6809-0.0925-0.0382-0.14990.0567-0.148-0.17820.21810.01220.24040.2876-0.01160.04140.2941-0.01620.2252-24.854-74.184-26.584
62.74330.31140.66925.7389-0.30964.65840.0586-0.13910.09870.23620.02140.1013-0.3266-0.0166-0.080.23050.02170.01440.260800.012534.966-42.683-1.518
73.6989-0.97290.32624.55330.81194.6820.031-0.1627-0.04020.09790.1042-0.18760.17260.1053-0.13510.2678-0.03640.01050.2554-0.00380.09638.28-84.421-10.495
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1514 - 1577
2X-RAY DIFFRACTION1B2 - 13
3X-RAY DIFFRACTION2C1514 - 1577
4X-RAY DIFFRACTION2D2 - 13
5X-RAY DIFFRACTION3E1514 - 1577
6X-RAY DIFFRACTION3F2 - 13
7X-RAY DIFFRACTION4G1514 - 1577
8X-RAY DIFFRACTION4H2 - 13
9X-RAY DIFFRACTION5I1514 - 1577
10X-RAY DIFFRACTION5J2 - 13
11X-RAY DIFFRACTION6K1514 - 1577
12X-RAY DIFFRACTION6L2 - 13
13X-RAY DIFFRACTION7M1514 - 1577
14X-RAY DIFFRACTION7N2 - 13

+
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