[English] 日本語
Yorodumi
- PDB-5buz: Crystal Structure of a Complex Between the SNARE Vam3 and the HOP... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5buz
TitleCrystal Structure of a Complex Between the SNARE Vam3 and the HOPS Vps33-Vps16 subcomplex from Chaetomium thermophilum
Components
  • Putative vacuolar protein sorting-associated protein
  • SM (Sec1/Munc18-like) protein
  • SNAP receptor-like protein
KeywordsTRANSPORT PROTEIN / Membrane trafficking / SM protein / HOPS complex / thermophile / SNARE domain
Function / homology
Function and homology information


HOPS complex / Golgi to vacuole transport / vacuole fusion, non-autophagic / vesicle docking / SNARE complex / SNAP receptor activity / vesicle fusion / endosomal transport / ligase activity / vesicle-mediated transport ...HOPS complex / Golgi to vacuole transport / vacuole fusion, non-autophagic / vesicle docking / SNARE complex / SNAP receptor activity / vesicle fusion / endosomal transport / ligase activity / vesicle-mediated transport / endomembrane system / SNARE binding / intracellular protein transport / actin binding / endosome
Similarity search - Function
Syntaxin-like protein / Sec1/Munc18 (SM) protein, domain 3b / Vps16, C-terminal / Vps16, N-terminal / Vacuolar protein sorting-associated protein 16 / Vps16, C-terminal domain superfamily / Vps16, C-terminal region / Vps16, N-terminal region / Vacuolar protein sorting-associated protein 33, domain 3b / Sec1/Munc18 (SM) protein, domain 2 ...Syntaxin-like protein / Sec1/Munc18 (SM) protein, domain 3b / Vps16, C-terminal / Vps16, N-terminal / Vacuolar protein sorting-associated protein 16 / Vps16, C-terminal domain superfamily / Vps16, C-terminal region / Vps16, N-terminal region / Vacuolar protein sorting-associated protein 33, domain 3b / Sec1/Munc18 (SM) protein, domain 2 / Syntaxin Binding Protein 1; Chain A, domain 2 / Sec1/Munc18 (SM) protein, domain 3a / Sec1/Munc18 (SM) protein, domain 1 / Sec1-like, domain 1 / Sec1-like protein / Sec1-like, domain 2 / Sec1-like superfamily / Sec1-like, domain 3a / Sec1 family / Syntaxin N-terminal domain / Syntaxin, N-terminal domain / SNARE domain / Syntaxin / Syntaxin/epimorphin, conserved site / Syntaxin / epimorphin family signature. / SNARE / Helical region found in SNAREs / t-SNARE coiled-coil homology domain profile. / Target SNARE coiled-coil homology domain / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme/RWD-like / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / WD40/YVTN repeat-like-containing domain superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
SNAP receptor-like protein / Probable vacuolar protein sorting-associated protein 16 homolog / Small conjugating protein ligase-like protein
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.1 Å
AuthorsBaker, R.W. / Jeffrey, P.D. / Hughson, F.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM071574 United States
Citation
Journal: Science / Year: 2015
Title: A direct role for the Sec1/Munc18-family protein Vps33 as a template for SNARE assembly.
Authors: Baker, R.W. / Jeffrey, P.D. / Zick, M. / Phillips, B.P. / Wickner, W.T. / Hughson, F.M.
#1: Journal: Plos One / Year: 2013
Title: Crystal Structures of the Sec1/Munc18 (SM) Protein Vps33, Alone and Bound to the Homotypic Fusion and Vacuolar Protein Sorting (HOPS) Subunit Vps16*
Authors: Baker, R.W. / Jeffrey, P.D. / Hughson, F.M.
History
DepositionJun 4, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 16, 2015Group: Database references
Revision 1.2Nov 22, 2017Group: Database references / Derived calculations / Refinement description
Category: citation / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Jan 17, 2018Group: Author supporting evidence / Category: pdbx_audit_support
Item: _pdbx_audit_support.country / _pdbx_audit_support.funding_organization
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: SM (Sec1/Munc18-like) protein
B: Putative vacuolar protein sorting-associated protein
C: SNAP receptor-like protein
D: SM (Sec1/Munc18-like) protein
E: Putative vacuolar protein sorting-associated protein
F: SNAP receptor-like protein


Theoretical massNumber of molelcules
Total (without water)238,8136
Polymers238,8136
Non-polymers00
Water00
1
A: SM (Sec1/Munc18-like) protein
B: Putative vacuolar protein sorting-associated protein
C: SNAP receptor-like protein


Theoretical massNumber of molelcules
Total (without water)119,4073
Polymers119,4073
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6300 Å2
ΔGint-31 kcal/mol
Surface area45100 Å2
MethodPISA
2
D: SM (Sec1/Munc18-like) protein
E: Putative vacuolar protein sorting-associated protein
F: SNAP receptor-like protein


Theoretical massNumber of molelcules
Total (without water)119,4073
Polymers119,4073
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6410 Å2
ΔGint-35 kcal/mol
Surface area45190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.039, 95.950, 164.060
Angle α, β, γ (deg.)90.000, 99.120, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain D
12chain B
22chain E
13chain C
23chain F

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALALYSLYSchain AAA5 - 6587 - 660
21ALAALALYSLYSchain DDD5 - 6587 - 660
12SERSERGLYGLYchain BBB505 - 8284 - 327
22SERSERGLYGLYchain EEE505 - 8284 - 327
13GLUGLUGLUGLUchain CCC188 - 22510 - 47
23GLUGLUGLUGLUchain FFF186 - 2258 - 47

NCS ensembles :
ID
1
2
3

-
Components

#1: Protein SM (Sec1/Munc18-like) protein / VPS33


Mass: 73990.117 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0057760 / Plasmid: pQLinkH / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: G0SCM5
#2: Protein Putative vacuolar protein sorting-associated protein / Vps16


Mass: 37912.211 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0026760 / Plasmid: pQLinkH / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: G0S6M7
#3: Protein SNAP receptor-like protein / VAM3


Mass: 7504.194 Da / Num. of mol.: 2 / Fragment: SNARE domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0015850 / Plasmid: pQLinkH / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: G0S236
Sequence detailsAuthors have indicated that the sequences in UniProt entries G0SCM5_CHATD and G0S236_CHATD are not correct

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.09 Å3/Da / Density % sol: 60.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: HEPES buffer, 8-10% w/v PEG 5000 monomethyl ether

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 2, 2014
RadiationMonochromator: Silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 54752 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 89.86 Å2 / Rmerge(I) obs: 0.102 / Χ2: 1.304 / Net I/av σ(I): 14.012 / Net I/σ(I): 6.3 / Num. measured all: 199852
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
3.1-3.153.60.86126870.49499.9
3.15-3.213.60.75927220.51499.9
3.21-3.273.70.66427250.512100
3.27-3.343.70.52127720.53899.9
3.34-3.413.70.40726790.57100
3.41-3.493.70.35327150.62299.9
3.49-3.583.70.29327480.712100
3.58-3.683.70.22426960.792100
3.68-3.783.70.19427130.896100
3.78-3.913.70.16627581.093100
3.91-4.043.70.14627231.222100
4.04-4.213.70.13127361.521100
4.21-4.43.70.11627421.821100
4.4-4.633.60.10927202.087100
4.63-4.923.60.09927392.19699.9
4.92-5.33.60.09727462.059100
5.3-5.833.60.09127401.749100
5.83-6.673.50.08127571.779100
6.67-8.43.70.06127792.258100
8.4-503.50.04128552.68699.8

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
CBASSdata collection
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4KMO

4kmo


Resolution: 3.1→47.975 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.233 2639 4.97 %Random selection
Rwork0.1935 50487 --
obs0.1955 53126 99.92 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 300.87 Å2 / Biso mean: 104.7949 Å2 / Biso min: 35.85 Å2
Refinement stepCycle: final / Resolution: 3.1→47.975 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15276 0 0 0 15276
Num. residues----1936
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00315512
X-RAY DIFFRACTIONf_angle_d0.79720932
X-RAY DIFFRACTIONf_chiral_restr0.0292376
X-RAY DIFFRACTIONf_plane_restr0.0032734
X-RAY DIFFRACTIONf_dihedral_angle_d15.1125848
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5769X-RAY DIFFRACTION7.271TORSIONAL
12D5769X-RAY DIFFRACTION7.271TORSIONAL
21B3063X-RAY DIFFRACTION7.271TORSIONAL
22E3063X-RAY DIFFRACTION7.271TORSIONAL
31C287X-RAY DIFFRACTION7.271TORSIONAL
32F287X-RAY DIFFRACTION7.271TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.1-3.15640.33171250.329226702795100
3.1564-3.21710.32511520.298126162768100
3.2171-3.28270.30331290.260526542783100
3.2827-3.35410.28691270.243826002727100
3.3541-3.43210.25071390.235526612800100
3.4321-3.51790.2561410.229826682809100
3.5179-3.6130.27221410.220726112752100
3.613-3.71930.27751280.2226822810100
3.7193-3.83930.26571290.201826532782100
3.8393-3.97640.26621200.201326672787100
3.9764-4.13550.21941530.185826372790100
4.1355-4.32360.19521350.17526512786100
4.3236-4.55140.22651660.174826392805100
4.5514-4.83630.20171400.161226332773100
4.8363-5.20930.22921320.177326782810100
5.2093-5.73280.2951410.195426652806100
5.7328-6.56060.24751370.210926772814100
6.5606-8.25880.22731440.186427002844100
8.2588-47.98070.17771600.15512725288599
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)
10.6204-0.12440.18871.73960.00811.3230.121-0.24020.05950.3156-0.140.1415-0.09090.012800.4696-0.04930.11050.5262-0.11250.4553.59164.9411180.7418
20.4497-0.5719-0.1790.0415-0.39640.39830.0090.036-0.07060.0447-0.00210.13770.173-0.223200.3766-0.0336-0.03450.6251-0.12960.7058-18.37-8.8023167.604
30.5128-0.6092-0.37391.1166-0.58941.2227-0.14470.234-0.0307-0.3810.0101-0.08710.10410.4517-0.00530.61440.0279-0.05750.7011-0.00160.39576.3444-7.7363144.4691
40.0828-0.2735-0.23580.86590.27590.462-0.03440.24020.1524-0.1467-0.01740.24130.2863-0.0695-00.5960.0195-0.00810.5271-0.110.57441.3591-26.5193160.2492
50.65330.1896-0.01910.9622-0.16680.82030.15740.2292-0.0294-0.1248-0.21910.22410.31740.108400.4161-0.01050.03270.5076-0.0160.50781.9224-14.436167.5278
60.32820.02450.01490.26870.33190.2746-0.4176-0.7883-0.1230.5614-0.3214-0.607-0.33550.7039-0.10280.5472-0.0558-0.00381.24740.34841.015138.6914-2.6114182.1717
70.4112-0.0774-0.20470.311-0.30380.5080.02070.08360.12640.0333-0.18090.18020.0740.04670.00020.6088-0.09690.00550.70610.00760.734625.23055.5844170.928
80.18040.14760.05060.07270.30120.5949-0.10340.00830.1763-0.1279-0.0468-0.3392-0.19040.6710.00010.8993-0.0382-0.07960.79230.07180.730623.523110.7524148.8538
90.8291-0.0292-0.05910.84720.17861.3449-0.6940.8640.5592-1.46920.6111-0.0254-0.0529-0.30420.50471.1984-0.3989-0.46811.1130.30220.4077-3.74494.1921127.8434
100.04840.02990.0055-0.00050.004-0.0269-0.38430.4457-0.5817-0.12980.33620.14720.008-0.0278-0.00021.5415-0.5726-0.42541.84150.07792.015-33.7266-14.9287120.4184
110.0337-0.0154-0.0736-0.00840.0231-0.01080.410.04330.12831.05220.0538-0.87440.2773-0.317901.0989-0.05980.05961.8528-0.011.0793-43.2933-0.1077187.3579
120.06760.04190.0910.1086-0.03020.275-0.16380.6557-0.30410.0927-0.61740.1626-0.2159-0.1597-0.00730.72750.2649-0.15591.1551-0.35171.5158-17.01959.9216174.4028
130.6349-0.1879-0.0991.436-0.33541.57730.011-0.13950.04350.37980.0071-0.03640.2725-0.0301-00.68880.0946-0.04690.50690.05990.48523.35743.2362101.1616
140.1308-0.5850.9729-0.00410.4663-0.2025-0.02680.41510.11010.14750.0521-0.145-0.14190.22320.00390.44350.03690.0010.62380.05720.721726.196614.983287.4833
150.538-0.28220.16021.6950.75711.8429-0.00730.09770.0183-0.27580.0044-0.1433-0.28230.083600.50990.05370.03770.36840.05470.54244.715421.148474.946
160.3209-0.52110.47290.8839-0.77860.74010.4033-0.7951-0.0330.19860.35560.99570.84230.39180.18170.45480.02050.13460.9997-0.32150.724-30.58788.7222102.844
170.216-0.0527-0.01130.19320.37350.8396-0.15320.1612-0.1814-0.3118-0.1151-0.24020.3577-0.517-0.00110.6924-0.0318-0.02620.448-0.03260.7875-17.26771.357891.3835
180.2414-0.0199-0.15450.0527-0.09860.3851-0.01280.2322-0.14850.402-0.01790.6540.3243-0.43520.00010.81790.0213-0.05090.47910.03830.7632-15.4276-5.24570.0752
190.24240.07250.11070.3071-0.38040.6752-0.20410.6514-0.2092-0.50440.1974-0.06480.55230.22570.00530.7770.19230.18590.7303-0.10420.63389.4704-4.211149.8001
200.05840.11560.04010.05820.14380.0543-0.36440.20630.30560.4337-0.1461-0.22430.8490.4878-0.00460.6585-0.09080.09861.62950.06441.088837.799614.441.8255
210.05020.11580.09190.0033-0.04870.05140.08460.2875-0.44520.06540.030.4251-0.19010.38980.00020.90220.1529-0.14781.49110.03481.224651.27127.0393109.8948
220.3056-0.0334-0.46870.1850.21750.8939-0.45990.02760.07150.628-0.4086-0.53630.3339-0.3483-0.04850.79790.1324-0.14621.16610.21511.203923.7584-3.117395.5413
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 215 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 216 through 379 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 380 through 479 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 480 through 565 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 566 through 658 )A0
6X-RAY DIFFRACTION6chain 'B' and (resid 505 through 544 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 545 through 605 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 606 through 657 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 658 through 790 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 791 through 828 )B0
11X-RAY DIFFRACTION11chain 'C' and (resid 188 through 212 )C0
12X-RAY DIFFRACTION12chain 'C' and (resid 213 through 225 )C0
13X-RAY DIFFRACTION13chain 'D' and (resid 5 through 215 )D0
14X-RAY DIFFRACTION14chain 'D' and (resid 216 through 379 )D0
15X-RAY DIFFRACTION15chain 'D' and (resid 380 through 658 )D0
16X-RAY DIFFRACTION16chain 'E' and (resid 505 through 546 )E0
17X-RAY DIFFRACTION17chain 'E' and (resid 547 through 605 )E0
18X-RAY DIFFRACTION18chain 'E' and (resid 606 through 657 )E0
19X-RAY DIFFRACTION19chain 'E' and (resid 658 through 769 )E0
20X-RAY DIFFRACTION20chain 'E' and (resid 770 through 828 )E0
21X-RAY DIFFRACTION21chain 'F' and (resid 186 through 212 )F0
22X-RAY DIFFRACTION22chain 'F' and (resid 213 through 225 )F0

+
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