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- PDB-5l2u: Oligomer crystal structure of CC chemokine 5 (CCL5) -

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Open data


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Basic information

Entry
Database: PDB / ID: 5l2u
TitleOligomer crystal structure of CC chemokine 5 (CCL5)
ComponentsC-C motif chemokine 5Chemokine
KeywordsCYTOKINE
Function / homology
Function and homology information


regulation of chronic inflammatory response / CCR4 chemokine receptor binding / chemokine receptor antagonist activity / activation of phospholipase D activity / positive regulation of cellular biosynthetic process / CCR1 chemokine receptor binding / positive regulation of natural killer cell chemotaxis / negative regulation of macrophage apoptotic process / chemokine receptor binding / positive regulation of cell-cell adhesion mediated by integrin ...regulation of chronic inflammatory response / CCR4 chemokine receptor binding / chemokine receptor antagonist activity / activation of phospholipase D activity / positive regulation of cellular biosynthetic process / CCR1 chemokine receptor binding / positive regulation of natural killer cell chemotaxis / negative regulation of macrophage apoptotic process / chemokine receptor binding / positive regulation of cell-cell adhesion mediated by integrin / positive regulation of activation of Janus kinase activity / receptor signaling protein tyrosine kinase activator activity / CCR5 chemokine receptor binding / positive regulation of T cell chemotaxis / positive regulation of homotypic cell-cell adhesion / negative regulation of G protein-coupled receptor signaling pathway / CCR chemokine receptor binding / lymphocyte chemotaxis / phosphatidylinositol phospholipase C activity / negative regulation of T cell apoptotic process / positive regulation of T cell apoptotic process / positive regulation of calcium ion transport / neutrophil activation / eosinophil chemotaxis / positive regulation of innate immune response / cellular response to fibroblast growth factor stimulus / chemokine-mediated signaling pathway / positive regulation of monocyte chemotaxis / Chemokine receptors bind chemokines / chemokine activity / dendritic cell chemotaxis / regulation of T cell activation / leukocyte cell-cell adhesion / negative regulation of viral genome replication / positive regulation of macrophage chemotaxis / phospholipase activator activity / positive regulation of smooth muscle cell migration / exocytosis / chemoattractant activity / macrophage chemotaxis / Interleukin-10 signaling / monocyte chemotaxis / regulation of insulin secretion / positive regulation of cell adhesion / negative regulation by host of viral transcription / positive regulation of T cell migration / positive regulation of translational initiation / cellular response to interleukin-1 / positive regulation of viral genome replication / positive regulation of T cell proliferation / positive regulation of phosphorylation / positive regulation of tyrosine phosphorylation of STAT protein / neutrophil chemotaxis / epithelial cell proliferation / positive regulation of epithelial cell proliferation / positive regulation of smooth muscle cell proliferation / positive regulation of receptor signaling pathway via JAK-STAT / response to virus / response to toxic substance / cellular response to virus / cellular response to type II interferon / intracellular calcium ion homeostasis / calcium ion transport / : / chemotaxis / cell-cell signaling / cellular response to tumor necrosis factor / G alpha (i) signalling events / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of ERK1 and ERK2 cascade / protein kinase activity / positive regulation of cell migration / inflammatory response / G protein-coupled receptor signaling pathway / protein homodimerization activity / extracellular space / extracellular region / identical protein binding / cytoplasm
Similarity search - Function
CC chemokine, conserved site / Small cytokines (intercrine/chemokine) C-C subfamily signature. / Chemokine beta/gamma/delta / Intercrine alpha family (small cytokine C-X-C) (chemokine CXC). / Chemokine interleukin-8-like domain / Chemokine interleukin-8-like superfamily / Small cytokines (intecrine/chemokine), interleukin-8 like / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #40 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
C-C motif chemokine 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 Å
AuthorsLiang, W. / Wang, A. / Tang, W.-J.
CitationJournal: To Be Published
Title: High resolution oligomer crystal structure of CC chemokine 5 (CCL5)
Authors: Liang, W. / Wang, A. / Tang, W.-J.
History
DepositionAug 2, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 9, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: C-C motif chemokine 5
B: C-C motif chemokine 5
C: C-C motif chemokine 5
D: C-C motif chemokine 5
E: C-C motif chemokine 5
F: C-C motif chemokine 5
G: C-C motif chemokine 5
H: C-C motif chemokine 5
I: C-C motif chemokine 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,60216
Polymers67,6329
Non-polymers9707
Water7,134396
1
A: C-C motif chemokine 5
B: C-C motif chemokine 5
C: C-C motif chemokine 5
D: C-C motif chemokine 5
E: C-C motif chemokine 5
F: C-C motif chemokine 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,82012
Polymers45,0886
Non-polymers7326
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10550 Å2
ΔGint-67 kcal/mol
Surface area19210 Å2
MethodPISA
2
G: C-C motif chemokine 5
H: C-C motif chemokine 5
I: C-C motif chemokine 5
hetero molecules

G: C-C motif chemokine 5
H: C-C motif chemokine 5
I: C-C motif chemokine 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5648
Polymers45,0886
Non-polymers4772
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z1
Buried area10090 Å2
ΔGint-50 kcal/mol
Surface area19590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.799, 210.082, 126.718
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222

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Components

#1: Protein
C-C motif chemokine 5 / Chemokine / EoCP / Eosinophil chemotactic cytokine / SIS-delta / Small-inducible cytokine A5 / T cell-specific ...EoCP / Eosinophil chemotactic cytokine / SIS-delta / Small-inducible cytokine A5 / T cell-specific protein P228 / TCP228 / T-cell-specific protein RANTES


Mass: 7514.645 Da / Num. of mol.: 9 / Fragment: UNP residues 27-91
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CCL5, D17S136E, SCYA5 / Production host: Escherichia coli (E. coli) / References: UniProt: P13501
#2: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 396 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 5.99 Å3/Da / Density % sol: 79.48 %
Crystal growTemperature: 303.15 K / Method: vapor diffusion, hanging drop / pH: 6.8 / Details: 0.1 HEPES, 300 mM NaCl, 3.5% 2-propanol / PH range: 6.8-7.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97926 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Jul 21, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 2.28→48.648 Å / Num. obs: 76849 / % possible obs: 99.8 % / Redundancy: 6.5 % / Net I/σ(I): 33.74

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CMD
Resolution: 2.28→48.648 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2091 3322 2.61 %
Rwork0.1785 --
obs0.1793 76849 88.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.28→48.648 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4701 0 59 396 5156
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084922
X-RAY DIFFRACTIONf_angle_d0.8816675
X-RAY DIFFRACTIONf_dihedral_angle_d14.3463071
X-RAY DIFFRACTIONf_chiral_restr0.053700
X-RAY DIFFRACTIONf_plane_restr0.005838
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.28-2.31260.3014610.2212447X-RAY DIFFRACTION42
2.3126-2.34710.2298650.20492817X-RAY DIFFRACTION48
2.3471-2.38380.2219930.19593303X-RAY DIFFRACTION57
2.3838-2.42280.2642980.19583700X-RAY DIFFRACTION64
2.4228-2.46460.21461190.18994341X-RAY DIFFRACTION75
2.4646-2.50940.17461310.21294788X-RAY DIFFRACTION81
2.5094-2.55770.28281330.20995019X-RAY DIFFRACTION87
2.5577-2.60990.22951440.20055263X-RAY DIFFRACTION90
2.6099-2.66670.23691480.20395493X-RAY DIFFRACTION95
2.6667-2.72870.23991480.20525647X-RAY DIFFRACTION97
2.7287-2.79690.22251520.20825797X-RAY DIFFRACTION99
2.7969-2.87250.24721680.2185774X-RAY DIFFRACTION100
2.8725-2.9570.26091620.21825793X-RAY DIFFRACTION99
2.957-3.05250.33461500.20735802X-RAY DIFFRACTION100
3.0525-3.16160.17691580.21185773X-RAY DIFFRACTION100
3.1616-3.28810.34641460.21125860X-RAY DIFFRACTION100
3.2881-3.43770.25321500.18685808X-RAY DIFFRACTION100
3.4377-3.61890.26831560.18355818X-RAY DIFFRACTION100
3.6189-3.84560.17911630.16455755X-RAY DIFFRACTION99
3.8456-4.14230.18191600.14755800X-RAY DIFFRACTION100
4.1423-4.55890.13061490.12685802X-RAY DIFFRACTION99
4.5589-5.21790.14851520.13795777X-RAY DIFFRACTION100
5.2179-6.57150.18231590.16055802X-RAY DIFFRACTION100
6.5715-48.65910.1641570.17165792X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
14.1904-0.6338-0.65340.5816-1.27193.96930.03450.1955-0.130.01860.03550.01970.12840.0561-0.06110.3416-0.20370.02480.25220.01820.23929.4733244.095532.7272
22.31341.21050.44761.63830.10782.25060.00160.1420.15980.00730.02650.05380.0067-0.0447-0.01930.3008-0.16650.05250.29080.03470.241230.6639246.473526.6516
36.0772-3.47661.73774.2229-0.74894.83170.038-0.3921-0.07330.0240.09150.31040.1288-0.2897-0.09720.2983-0.16550.05960.26550.04810.292227.9664241.996226.2687
43.81250.7273-0.66193.9665-5.4668.05440.03020.53520.2488-0.4002-0.1037-0.18350.44460.18060.04840.3006-0.14510.08320.4096-0.00790.303935.5202242.862217.3283
54.96894.63145.06128.90485.73456.9431-0.57060.5556-0.5635-1.11260.21961.38040.7983-1.15530.34460.6489-0.23670.04790.4169-0.03150.525824.2576243.528534.5682
61.53361.18680.05921.2312-0.36360.5383-0.044-0.0050.28690.09830.04020.3096-0.24720.0383-0.01390.4883-0.13080.04310.1790.02610.32125.6302260.758545.6669
73.5481-0.5623-0.43623.9356-0.44461.3152-0.00380.09670.1666-0.2260.08070.57-0.1378-0.0678-0.16980.4426-0.1590.01670.16360.01320.335420.5492253.890546.4265
85.11161.42780.13175.52110.08434.6168-0.22950.48350.4121-0.3320.10820.3131-0.2521-0.16650.09120.5617-0.14640.00340.22860.05850.29320.8556258.96345.3942
94.58156.1797-1.28088.5101-1.5463.89120.2019-0.52060.12711.0297-0.30790.68510.1025-0.23870.00830.6996-0.04760.22250.2327-0.010.453515.53257.52155.6087
104.3363-0.91040.44911.281-1.81273.0857-0.04350.10950.17270.0946-0.06120.21620.1334-0.03730.06080.4105-0.21830.01980.25790.01490.328916.8919229.514335.6504
113.30251.47270.52211.29980.25740.86290.1633-0.01380.12820.06530.01140.21610.0629-0.0361-0.08780.4328-0.2206-0.00080.30580.05090.258417.6737233.416130.8233
122.5496-3.7788-1.64566.32720.83174.6408-0.1974-0.2377-0.05730.12260.32670.34430.0859-0.0558-0.08540.4081-0.25490.06980.3175-0.02360.349913.0741229.945730.618
133.67632.80650.96414.5450.66921.3909-0.10970.1894-0.0531-0.23050.1787-0.01130.0233-0.00620.04010.5255-0.3517-0.00260.6254-0.01450.235816.4189231.775619.558
142.7434-0.3793-0.99832.23-1.34791.3773-0.0240.00960.20850.20130.03460.0527-0.01480.0537-0.00820.5238-0.1908-0.01310.23070.03360.326422.8236238.56149.1578
151.1078-0.5446-0.35924.260.01540.87740.047-0.03030.04680.03140.1130.2689-0.0523-0.0236-0.07470.5119-0.16780.04280.21580.02610.253218.7412236.275853.9817
162.8217-3.82491.64195.8567-1.35614.62010.21970.28010.31980.181-0.16780.1259-0.08590.0555-0.09870.5476-0.20530.00190.22350.06210.330419.6892241.418353.8442
172.7712.477-0.01117.0328-0.0781.07880.3972-0.2556-0.06410.648-0.23060.0023-0.09980.043-0.02330.8536-0.165-0.00110.2603-0.00260.209419.8193237.634564.6585
181.57880.03380.18081.7757-0.28810.90940.01730.00230.35450.2253-0.06920.2793-0.0304-0.0685-0.05390.3605-0.2083-0.0040.25720.03430.33562.8009220.909439.5044
194.7080.6341-1.40156.3835-0.00066.16310.0368-0.24560.03840.6099-0.11280.443-0.0268-0.35760.08570.4019-0.22840.04570.39860.04950.3167-1.6942220.272339.0698
204.9762.217-2.55672.389-0.83063.4044-0.33040.66460.4969-0.54720.10150.449-0.2223-0.16320.11310.3621-0.2199-0.12280.51980.15350.3977-2.7065225.171428.4846
211.0713-1.15320.00191.7338-1.40033.9701-0.0314-0.12590.25310.11710.0114-0.0486-0.08440.15480.0360.4649-0.1541-0.03560.21470.04040.284716.4031220.548851.883
220.80340.3115-0.37082.6851-0.22951.89610.0025-0.0461-0.05450.1540.04240.0969-0.0477-0.02990.02320.4152-0.09010.0070.15310.06620.257514.0818217.990557.7652
238.5361-4.5485-1.42266.61440.28275.17450.34230.23860.3222-0.1407-0.2637-0.0354-0.3008-0.0673-0.06680.429-0.13490.01550.15190.06330.251116.6424222.54558.1711
244.2035.3928-4.19187.4308-5.12324.5316-0.1589-0.5372-0.36720.4835-0.04560.06380.10290.5150.12570.5282-0.0275-0.04610.23310.08030.297819.9179215.634267.1384
251.13210.9613-1.50492.54790.01412.96450.10350.0260.02510.1784-0.1082-0.23640.10540.2404-0.00370.1392-0.05310.01180.49830.05150.281447.842253.63069.8404
262.84340.79190.1871.14850.38192.16430.11560.01690.10890.0841-0.02070.1405-0.0830.0174-0.0220.1457-0.05540.05680.44770.04190.232644.3624254.381115.5008
273.8112.9536-0.40213.3721.57385.8523-0.19340.10690.1478-0.33080.2682-0.1802-0.26070.2964-0.06910.1166-0.03380.0290.4340.04480.297849.573254.361915.9571
283.884-2.7875-5.63394.81442.9219.0344-0.0958-0.3713-0.14130.6242-0.09530.26360.45270.37710.13570.2636-0.12790.04460.51920.07040.2745.2258248.146324.9037
293.7113-0.0832-0.86632.0419-0.06841.04760.094-0.12130.41170.0297-0.1233-0.1061-0.08460.0107-0.02270.12410.06110.02810.50620.02780.300840.9026265.0267-3.0216
309.1265-0.0411-1.36293.03180.29923.6068-0.0064-0.76010.44160.2402-0.05040.1463-0.1750.1714-0.02940.15660.07110.04950.5366-0.01260.269539.2837269.4369-3.1352
315.88141.9967-1.78015.00811.01073.63290.08290.99150.7555-0.4685-0.1817-0.1094-0.20130.20250.04290.28380.18770.07050.62310.20050.43142.3222273.041-13.5081
321.98691.6922-0.82272.67211.35723.7802-0.0166-0.14270.36790.045-0.1624-0.0282-0.09690.03640.16010.1418-0.00770.01510.5993-0.00690.328765.9331257.71056.4503
333.20161.4648-0.26511.73250.05110.58930.07030.07230.23890.04270.070.1022-0.04090.0628-0.02470.146-0.05350.04310.5671-0.02960.254162.5762259.5511.7935
343.6205-0.201-0.11098.3992-1.59974.22340.1071-0.17170.2204-0.4067-0.027-0.1860.0230.0928-0.07450.123-0.05330.0160.62130.03370.292567.5421261.31511.6301
351.97340.76490.15712.35880.64731.18710.075-0.75820.04770.14660.0526-0.07120.02190.0217-0.03650.2763-0.1896-0.01220.85250.00120.247964.2736259.359722.6234
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 20 )
2X-RAY DIFFRACTION2chain 'A' and (resid 21 through 43 )
3X-RAY DIFFRACTION3chain 'A' and (resid 44 through 55 )
4X-RAY DIFFRACTION4chain 'A' and (resid 56 through 68 )
5X-RAY DIFFRACTION5chain 'B' and (resid 4 through 8 )
6X-RAY DIFFRACTION6chain 'B' and (resid 9 through 20 )
7X-RAY DIFFRACTION7chain 'B' and (resid 21 through 43 )
8X-RAY DIFFRACTION8chain 'B' and (resid 44 through 55 )
9X-RAY DIFFRACTION9chain 'B' and (resid 56 through 68 )
10X-RAY DIFFRACTION10chain 'C' and (resid 4 through 20 )
11X-RAY DIFFRACTION11chain 'C' and (resid 21 through 43 )
12X-RAY DIFFRACTION12chain 'C' and (resid 44 through 55 )
13X-RAY DIFFRACTION13chain 'C' and (resid 56 through 68 )
14X-RAY DIFFRACTION14chain 'D' and (resid 5 through 20 )
15X-RAY DIFFRACTION15chain 'D' and (resid 21 through 43 )
16X-RAY DIFFRACTION16chain 'D' and (resid 44 through 55 )
17X-RAY DIFFRACTION17chain 'D' and (resid 56 through 68 )
18X-RAY DIFFRACTION18chain 'E' and (resid 4 through 43 )
19X-RAY DIFFRACTION19chain 'E' and (resid 44 through 55 )
20X-RAY DIFFRACTION20chain 'E' and (resid 56 through 68 )
21X-RAY DIFFRACTION21chain 'F' and (resid 5 through 20 )
22X-RAY DIFFRACTION22chain 'F' and (resid 21 through 43 )
23X-RAY DIFFRACTION23chain 'F' and (resid 44 through 55 )
24X-RAY DIFFRACTION24chain 'F' and (resid 56 through 68 )
25X-RAY DIFFRACTION25chain 'G' and (resid 5 through 20 )
26X-RAY DIFFRACTION26chain 'G' and (resid 21 through 43 )
27X-RAY DIFFRACTION27chain 'G' and (resid 44 through 55 )
28X-RAY DIFFRACTION28chain 'G' and (resid 56 through 68 )
29X-RAY DIFFRACTION29chain 'H' and (resid 5 through 38 )
30X-RAY DIFFRACTION30chain 'H' and (resid 39 through 55 )
31X-RAY DIFFRACTION31chain 'H' and (resid 56 through 68 )
32X-RAY DIFFRACTION32chain 'I' and (resid 4 through 20 )
33X-RAY DIFFRACTION33chain 'I' and (resid 21 through 43 )
34X-RAY DIFFRACTION34chain 'I' and (resid 44 through 55 )
35X-RAY DIFFRACTION35chain 'I' and (resid 56 through 68 )

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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

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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

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