[English] 日本語
Yorodumi
- PDB-4uj3: Crystal structure of human Rab11-Rabin8-FIP3 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4uj3
TitleCrystal structure of human Rab11-Rabin8-FIP3
Components
  • RAB-3A-INTERACTING PROTEIN
  • RAB11 FAMILY-INTERACTING PROTEIN 3
  • RAS-RELATED PROTEIN RAB-11A
KeywordsTRANSPORT PROTEIN / CILIARY TARGETING COMPLEX / CILIUM / VESICULAR TRANSPORT / MEMBRANE TRAFFICKING
Function / homology
Function and homology information


ciliary basal body-plasma membrane docking / protein localization to motile cilium / regulation of early endosome to recycling endosome transport / regulation of protein localization to centrosome / protein localization to cleavage furrow / regulation of endocytic recycling / early endosome to recycling endosome transport / postsynaptic recycling endosome membrane / negative regulation of filopodium assembly / establishment of protein localization to organelle ...ciliary basal body-plasma membrane docking / protein localization to motile cilium / regulation of early endosome to recycling endosome transport / regulation of protein localization to centrosome / protein localization to cleavage furrow / regulation of endocytic recycling / early endosome to recycling endosome transport / postsynaptic recycling endosome membrane / negative regulation of filopodium assembly / establishment of protein localization to organelle / protein localization to organelle / establishment of vesicle localization / plasma membrane to endosome transport / negative regulation of adiponectin secretion / postsynaptic recycling endosome / positive regulation of mitotic cytokinetic process / regulation of cilium assembly / exosomal secretion / amyloid-beta clearance by transcytosis / astral microtubule organization / neurotransmitter receptor transport, endosome to postsynaptic membrane / VxPx cargo-targeting to cilium / protein transmembrane transport / regulation of vesicle-mediated transport / BBSome-mediated cargo-targeting to cilium / Golgi to plasma membrane transport / myosin V binding / positive regulation of cilium assembly / RAB geranylgeranylation / Golgi to plasma membrane protein transport / melanosome transport / proximal dendrite / multivesicular body assembly / protein localization to cilium / RAB GEFs exchange GTP for GDP on RABs / endocytic recycling / establishment of protein localization to membrane / syntaxin binding / TBC/RABGAPs / protein localization to cell surface / protein targeting to membrane / dynein light intermediate chain binding / mitotic metaphase chromosome alignment / exocytosis / cleavage furrow / positive regulation of epithelial cell migration / endocytic vesicle / cilium assembly / mitotic spindle assembly / intercellular bridge / transport vesicle / vesicle-mediated transport / phagocytic vesicle / positive regulation of G2/M transition of mitotic cell cycle / multivesicular body / centriole / Anchoring of the basal body to the plasma membrane / cytoplasmic vesicle membrane / guanyl-nucleotide exchange factor activity / regulation of cytokinesis / small monomeric GTPase / trans-Golgi network membrane / protein localization to plasma membrane / Translocation of SLC2A4 (GLUT4) to the plasma membrane / trans-Golgi network / recycling endosome / small GTPase binding / centriolar satellite / recycling endosome membrane / spindle pole / neuron projection development / Vasopressin regulates renal water homeostasis via Aquaporins / endocytic vesicle membrane / protein transport / lamellipodium / G protein activity / GTPase binding / midbody / cytoplasmic vesicle / protein-macromolecule adaptor activity / microtubule binding / molecular adaptor activity / vesicle / endosome / ciliary basal body / cilium / Golgi membrane / cell division / intracellular membrane-bounded organelle / GTPase activity / centrosome / calcium ion binding / protein-containing complex binding / GTP binding / perinuclear region of cytoplasm / glutamatergic synapse / Golgi apparatus / protein homodimerization activity / protein-containing complex / mitochondrion
Similarity search - Function
: / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2440 / GDP/GTP exchange factor Sec2, N-terminal / Rab-binding domain FIP-RBD / FIP-RBD, C-terminal domain superfamily / Guanine nucleotide exchange factor RAB3IL/RAB3IP/Sec2 / GDP/GTP exchange factor Sec2p / FIP domain / FIP-RBD domain profile. / : ...: / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2440 / GDP/GTP exchange factor Sec2, N-terminal / Rab-binding domain FIP-RBD / FIP-RBD, C-terminal domain superfamily / Guanine nucleotide exchange factor RAB3IL/RAB3IP/Sec2 / GDP/GTP exchange factor Sec2p / FIP domain / FIP-RBD domain profile. / : / Small GTPase Rab domain profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / EF-hand domain pair / Rab subfamily of small GTPases / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / Up-down Bundle / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Rab11 family-interacting protein 3 / Ras-related protein Rab-11A / Rab-3A-interacting protein
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsVetter, M. / Lorentzen, E.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2015
Title: Structure of Rab11-Fip3-Rabin8 Reveals Simultaneous Binding of Fip3 and Rabin8 Effectors to Rab11.
Authors: Vetter, M. / Stehle, R. / Basquin, C. / Lorentzen, E.
History
DepositionApr 8, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 12, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 19, 2015Group: Database references
Revision 1.2Sep 16, 2015Group: Database references
Revision 1.3Jan 10, 2024Group: 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_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.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_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: RAS-RELATED PROTEIN RAB-11A
B: RAB-3A-INTERACTING PROTEIN
C: RAB11 FAMILY-INTERACTING PROTEIN 3
D: RAS-RELATED PROTEIN RAB-11A
E: RAB-3A-INTERACTING PROTEIN
F: RAB11 FAMILY-INTERACTING PROTEIN 3
G: RAS-RELATED PROTEIN RAB-11A
H: RAB-3A-INTERACTING PROTEIN
I: RAB11 FAMILY-INTERACTING PROTEIN 3
J: RAS-RELATED PROTEIN RAB-11A
K: RAB-3A-INTERACTING PROTEIN
L: RAB11 FAMILY-INTERACTING PROTEIN 3
M: RAS-RELATED PROTEIN RAB-11A
N: RAB-3A-INTERACTING PROTEIN
O: RAB11 FAMILY-INTERACTING PROTEIN 3
P: RAS-RELATED PROTEIN RAB-11A
Q: RAB-3A-INTERACTING PROTEIN
R: RAB11 FAMILY-INTERACTING PROTEIN 3
S: RAS-RELATED PROTEIN RAB-11A
T: RAB-3A-INTERACTING PROTEIN
U: RAB11 FAMILY-INTERACTING PROTEIN 3
V: RAS-RELATED PROTEIN RAB-11A
W: RAB-3A-INTERACTING PROTEIN
X: RAB11 FAMILY-INTERACTING PROTEIN 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)409,48942
Polymers404,82724
Non-polymers4,66218
Water1,946108
1
A: RAS-RELATED PROTEIN RAB-11A
B: RAB-3A-INTERACTING PROTEIN
C: RAB11 FAMILY-INTERACTING PROTEIN 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1505
Polymers50,6033
Non-polymers5472
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2670 Å2
ΔGint-20.9 kcal/mol
Surface area23760 Å2
MethodPQS
2
D: RAS-RELATED PROTEIN RAB-11A
E: RAB-3A-INTERACTING PROTEIN
F: RAB11 FAMILY-INTERACTING PROTEIN 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1505
Polymers50,6033
Non-polymers5472
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2520 Å2
ΔGint-21.8 kcal/mol
Surface area23930 Å2
MethodPQS
3
G: RAS-RELATED PROTEIN RAB-11A
H: RAB-3A-INTERACTING PROTEIN
I: RAB11 FAMILY-INTERACTING PROTEIN 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1505
Polymers50,6033
Non-polymers5472
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2750 Å2
ΔGint-21.6 kcal/mol
Surface area23120 Å2
MethodPQS
4
J: RAS-RELATED PROTEIN RAB-11A
K: RAB-3A-INTERACTING PROTEIN
L: RAB11 FAMILY-INTERACTING PROTEIN 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1505
Polymers50,6033
Non-polymers5472
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2600 Å2
ΔGint-23 kcal/mol
Surface area23120 Å2
MethodPQS
5
M: RAS-RELATED PROTEIN RAB-11A
N: RAB-3A-INTERACTING PROTEIN
O: RAB11 FAMILY-INTERACTING PROTEIN 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,2466
Polymers50,6033
Non-polymers6433
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2670 Å2
ΔGint-23.4 kcal/mol
Surface area23230 Å2
MethodPQS
6
P: RAS-RELATED PROTEIN RAB-11A
Q: RAB-3A-INTERACTING PROTEIN
R: RAB11 FAMILY-INTERACTING PROTEIN 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1505
Polymers50,6033
Non-polymers5472
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2490 Å2
ΔGint-21.8 kcal/mol
Surface area22970 Å2
MethodPQS
7
S: RAS-RELATED PROTEIN RAB-11A
T: RAB-3A-INTERACTING PROTEIN
U: RAB11 FAMILY-INTERACTING PROTEIN 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1505
Polymers50,6033
Non-polymers5472
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2760 Å2
ΔGint-22.3 kcal/mol
Surface area23170 Å2
MethodPQS
8
V: RAS-RELATED PROTEIN RAB-11A
W: RAB-3A-INTERACTING PROTEIN
X: RAB11 FAMILY-INTERACTING PROTEIN 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,3446
Polymers50,6033
Non-polymers7413
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3040 Å2
ΔGint-20.1 kcal/mol
Surface area21830 Å2
MethodPQS
Unit cell
Length a, b, c (Å)67.498, 165.374, 218.687
Angle α, β, γ (deg.)90.00, 95.93, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
33
/ NCS ensembles :
ID
1
2
3

-
Components

-
Protein , 3 types, 24 molecules ADGJMPSVBEHKNQTWCFILORUX

#1: Protein
RAS-RELATED PROTEIN RAB-11A / RAB-11 / YL8 / RAB11A


Mass: 21116.736 Da / Num. of mol.: 8 / Fragment: GTPASE DOMAIN / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P62491
#2: Protein
RAB-3A-INTERACTING PROTEIN / RAB3A-INTERACTING PROTEIN / RABIN-3 / SSX2-INTERACTING PROTEIN / RABIN8


Mass: 22217.479 Da / Num. of mol.: 8 / Fragment: C-TERMINAL DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q96QF0
#3: Protein
RAB11 FAMILY-INTERACTING PROTEIN 3 / FIP3-RAB11 / RAB11-FIP3 / ARFOPHILIN-1 / EF HANDS-CONTAINING RAB-INTERACTING PROTEIN / EFERIN / MU- ...FIP3-RAB11 / RAB11-FIP3 / ARFOPHILIN-1 / EF HANDS-CONTAINING RAB-INTERACTING PROTEIN / EFERIN / MU-MB-17.148 / FIP3


Mass: 7269.180 Da / Num. of mol.: 8 / Fragment: C-TERMINAL DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O75154

-
Non-polymers , 5 types, 126 molecules

#4: Chemical
ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 108 / 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: 3 Å3/Da / Density % sol: 59 % / Description: NONE
Crystal growpH: 5.6
Details: 50MM MES PH 5.6, 0.2M AMMONIUM SULFATE AND 12% PEG 8000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 92398 / % possible obs: 95 % / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 19
Reflection shellResolution: 2.97→3.14 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 1.8 / % possible all: 94

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: DEV_1647)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1YZK

1yzk


Resolution: 3→48.543 Å / SU ML: 0.48 / σ(F): 1.33 / Phase error: 27.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2504 9297 5 %
Rwork0.1979 --
obs0.2005 92398 98.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3→48.543 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22924 0 282 108 23314
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00523670
X-RAY DIFFRACTIONf_angle_d0.9932136
X-RAY DIFFRACTIONf_dihedral_angle_d13.5928472
X-RAY DIFFRACTIONf_chiral_restr0.0393692
X-RAY DIFFRACTIONf_plane_restr0.0044055
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.03410.37563140.3545970X-RAY DIFFRACTION100
3.0341-3.06980.39493180.3416024X-RAY DIFFRACTION100
3.0698-3.10720.37463050.33335822X-RAY DIFFRACTION100
3.1072-3.14650.38343140.31865914X-RAY DIFFRACTION100
3.1465-3.18790.38963230.31556093X-RAY DIFFRACTION100
3.1879-3.23160.36933080.30585905X-RAY DIFFRACTION100
3.2316-3.27780.3353070.29155861X-RAY DIFFRACTION100
3.2778-3.32670.33453140.28355960X-RAY DIFFRACTION100
3.3267-3.37860.3283210.25096024X-RAY DIFFRACTION99
3.3786-3.4340.31273140.24785894X-RAY DIFFRACTION100
3.434-3.49320.31933050.23445832X-RAY DIFFRACTION100
3.4932-3.55670.29963220.22946097X-RAY DIFFRACTION100
3.5567-3.62510.28443080.22745811X-RAY DIFFRACTION99
3.6251-3.69910.30013120.21975915X-RAY DIFFRACTION99
3.6991-3.77950.25983100.21725875X-RAY DIFFRACTION99
3.7795-3.86740.26323030.20645814X-RAY DIFFRACTION98
3.8674-3.9640.27973140.2095938X-RAY DIFFRACTION97
3.964-4.07120.27073040.20625693X-RAY DIFFRACTION98
4.0712-4.19090.2673110.18135861X-RAY DIFFRACTION97
4.1909-4.32610.21852980.16935741X-RAY DIFFRACTION97
4.3261-4.48060.21623180.16775954X-RAY DIFFRACTION98
4.4806-4.65990.21463050.15855713X-RAY DIFFRACTION98
4.6599-4.87170.2253100.1565905X-RAY DIFFRACTION98
4.8717-5.12830.21683120.16225853X-RAY DIFFRACTION98
5.1283-5.44920.23773070.16855787X-RAY DIFFRACTION98
5.4492-5.86930.23992980.18255833X-RAY DIFFRACTION98
5.8693-6.45880.21833060.17985838X-RAY DIFFRACTION98
6.4588-7.39050.22723030.17065791X-RAY DIFFRACTION97
7.3905-9.30060.17422930.14385674X-RAY DIFFRACTION95
9.3006-48.5490.19823200.17985902X-RAY DIFFRACTION99

+
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