[English] 日本語
Yorodumi
- PDB-5jtw: Crystal structure of complement C4b re-refined using iMDFF -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5jtw
TitleCrystal structure of complement C4b re-refined using iMDFF
Components(Complement C4-A) x 3
KeywordsIMMUNE SYSTEM / innate immune system / complement / active form
Function / homology
Function and homology information


complement component C1q complex binding / positive regulation of apoptotic cell clearance / Activation of C3 and C5 / complement activation / endopeptidase inhibitor activity / Initial triggering of complement / complement activation, classical pathway / Regulation of Complement cascade / Post-translational protein phosphorylation / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) ...complement component C1q complex binding / positive regulation of apoptotic cell clearance / Activation of C3 and C5 / complement activation / endopeptidase inhibitor activity / Initial triggering of complement / complement activation, classical pathway / Regulation of Complement cascade / Post-translational protein phosphorylation / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / blood microparticle / endoplasmic reticulum lumen / inflammatory response / axon / innate immune response / neuronal cell body / synapse / dendrite / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
: / : / Complement C4, MG1 domain / Complement C4A/B CUB C-terminal domain / Jelly Rolls - #1540 / N-terminal domain of TfIIb - #160 / S-adenosyl-L-methionine-dependent methyltransferases - #20 / S-adenosyl-L-methionine-dependent methyltransferases / Macroglobulin (MG2) domain / Immunoglobulin-like - #1940 ...: / : / Complement C4, MG1 domain / Complement C4A/B CUB C-terminal domain / Jelly Rolls - #1540 / N-terminal domain of TfIIb - #160 / S-adenosyl-L-methionine-dependent methyltransferases - #20 / S-adenosyl-L-methionine-dependent methyltransferases / Macroglobulin (MG2) domain / Immunoglobulin-like - #1940 / N-terminal domain of TfIIb / Alpha-2-macroglobulin, conserved site / Alpha-2-macroglobulin family thiolester region signature. / Anaphylatoxin, complement system domain / : / Alpha-macro-globulin thiol-ester bond-forming region / Anaphylatoxin domain signature. / Anaphylatoxin, complement system / Anaphylatoxin/fibulin / Anaphylotoxin-like domain / Anaphylatoxin domain profile. / Anaphylatoxin homologous domain / Netrin C-terminal Domain / Netrin module, non-TIMP type / UNC-6/NTR/C345C module / Glycosyltransferase - #20 / Macroglobulin domain MG4 / Macroglobulin domain MG4 / Alpha-macroglobulin, receptor-binding / Alpha-macroglobulin, receptor-binding domain superfamily / Macroglobulin domain MG3 / : / A-macroglobulin receptor binding domain / Macroglobulin domain MG3 / A-macroglobulin receptor / Netrin domain / NTR domain profile. / Alpha-2-macroglobulin / Macroglobulin domain / Tissue inhibitor of metalloproteinases-like, OB-fold / Alpha-2-macroglobulin, bait region domain / Alpha-macroglobulin-like, TED domain / Alpha-2-macroglobulin family / MG2 domain / A-macroglobulin TED domain / Alpha-2-macroglobulin bait region domain / Alpha-2-Macroglobulin / Alpha-2-macroglobulin family / Other non-globular / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid / Glycosyltransferase / Alpha/alpha barrel / Single Sheet / Special / Jelly Rolls / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsCroll, T.I. / Andersen, G.R.
Funding support Denmark, 2items
OrganizationGrant numberCountry
Aarhus University Research Foundation Denmark
Danish Science Research Council for Nature and Universe Denmark
Citation
Journal: Acta Crystallogr D Struct Biol / Year: 2016
Title: Re-evaluation of low-resolution crystal structures via interactive molecular-dynamics flexible fitting (iMDFF): a case study in complement C4.
Authors: Croll, T.I. / Andersen, G.R.
#1: Journal: J Immunol. / Year: 2015
Title: Structural Basis for the Function of Complement Component C4 within the Classical and Lectin Pathways of Complement.
Authors: Mortensen, S. / Kidmose, R.T. / Petersen, S.V. / Szilagyi, A. / Prohaszka, Z. / Andersen, G.R.
History
DepositionMay 9, 2016Deposition site: RCSB / Processing site: PDBE
SupersessionAug 10, 2016ID: 4xam
Revision 1.0Aug 10, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 17, 2016Group: Structure summary
Revision 1.2Sep 14, 2016Group: Database references
Revision 1.3Sep 28, 2016Group: Database references
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.6Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Complement C4-A
B: Complement C4-A
C: Complement C4-A
D: Complement C4-A
E: Complement C4-A
F: Complement C4-A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)361,65710
Polymers360,7736
Non-polymers8854
Water00
1
A: Complement C4-A
B: Complement C4-A
C: Complement C4-A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,8295
Polymers180,3863
Non-polymers4422
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17180 Å2
ΔGint-83 kcal/mol
Surface area69380 Å2
MethodPISA
2
D: Complement C4-A
E: Complement C4-A
F: Complement C4-A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,8295
Polymers180,3863
Non-polymers4422
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17280 Å2
ΔGint-81 kcal/mol
Surface area68700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.500, 161.080, 131.600
Angle α, β, γ (deg.)90.000, 107.260, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Complement C4-A / Acidic complement C4 / C3 and PZP-like alpha-2-macroglobulin domain-containing protein 2


Mass: 71761.688 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P0C0L4
#2: Protein Complement C4-A / Acidic complement C4 / C3 and PZP-like alpha-2-macroglobulin domain-containing protein 2


Mass: 75508.938 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P0C0L4
#3: Protein Complement C4-A / Acidic complement C4 / C3 and PZP-like alpha-2-macroglobulin domain-containing protein 2


Mass: 33115.629 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P0C0L4
#4: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.41 Å3/Da / Density % sol: 63.92 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7
Details: the crystals appeared after mixing C4b at 4 mg/ml in 20 mM HEPES pH 7.5, 100 mM sodium chloride with 100 mM HEPES pH 7.0, 400 mM magnesium chloride, 7.5% PEG8000 and a microseeding stock at ...Details: the crystals appeared after mixing C4b at 4 mg/ml in 20 mM HEPES pH 7.5, 100 mM sodium chloride with 100 mM HEPES pH 7.0, 400 mM magnesium chloride, 7.5% PEG8000 and a microseeding stock at the volume ration 1:1:0.5. The crystals appeared in 1-2 weeks and reached the final size in 1 month

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.984 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 14, 2014
RadiationMonochromator: Silicon (1 1 1) channel-cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.984 Å / Relative weight: 1
ReflectionResolution: 3.5→49.54 Å / Num. obs: 60261 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Redundancy: 7.14 % / Biso Wilson estimate: 101.32 Å2 / CC1/2: 0.949 / Rmerge(I) obs: 0.492 / Net I/σ(I): 4.55
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
3.5-3.593.1330.65199.3
3.59-3.682.5910.8199.5
3.68-3.792.2690.89199.4
3.79-3.921.831.09198.9
3.92-4.061.3871.41198.2
4.06-4.211.0451.8198.6
4.21-4.40.7632.62199.4
4.4-4.640.5343.59199.2
4.64-4.930.4114.59198.6
4.93-5.310.3794.87198.2
5.31-5.850.3554.98198.6
5.85-6.690.3155.92198.6
6.69-8.420.1749.53197.6
8.420.07320.82196.1

-
Processing

Software
NameVersionClassification
PHENIXdev_2376refinement
PDB_EXTRACT3.2data extraction
XDSNovember 11, 2013data reduction
XSCALEOct 15, 2015data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4xam

4xam
PDB Unreleased entry


Resolution: 3.5→49.376 Å / SU ML: 0.6 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 32.55
RfactorNum. reflection% reflection
Rfree0.2935 2014 3.34 %
Rwork0.248 --
obs0.2495 60234 98.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 289.39 Å2 / Biso mean: 122.3647 Å2 / Biso min: 33.53 Å2
Refinement stepCycle: final / Resolution: 3.5→49.376 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24256 0 56 0 24312
Biso mean--152.13 --
Num. residues----3128
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00324860
X-RAY DIFFRACTIONf_angle_d0.82633760
X-RAY DIFFRACTIONf_chiral_restr0.0473798
X-RAY DIFFRACTIONf_plane_restr0.0094390
X-RAY DIFFRACTIONf_dihedral_angle_d14.34714998
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.5-3.58750.3621430.34344202434599
3.5875-3.68450.39141480.33424135428399
3.6845-3.79290.33751430.333841844327100
3.7929-3.91520.37821330.32284179431299
3.9152-4.05510.40691480.31464129427798
4.0551-4.21740.35961500.28444090424099
4.2174-4.40920.32311330.26524207434099
4.4092-4.64150.29061500.23464155430599
4.6415-4.93210.21831380.21024146428499
4.9321-5.31250.31581450.22054161430698
5.3125-5.84630.2771470.23474136428399
5.8463-6.69050.30341400.24174201434199
6.6905-8.42260.29621490.22384134428398
8.4226-49.38050.19681470.18914161430897
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)
13.5629-0.03111.7834.3609-0.59566.31820.17720.26620.0979-0.1012-0.6194-1.20440.58671.05210.35720.81480.317-0.04921.01660.02471.03918.9984-6.9388-33.856
23.31451.74891.78418.1469-0.25773.36030.10350.5055-0.07570.32280.0837-1.2530.02410.78730.06850.43470.01420.09850.83640.00150.7313-9.338723.6542-48.2417
33.0166-0.3746-0.37526.16432.32751.9495-0.0950.1304-0.4138-0.7417-0.052-0.1964-0.03991.08130.09931.2630.0851-0.12611.17430.06950.7125-18.466219.2084-83.9103
42.04870.0791.28313.4184-1.49651.50070.45031.1999-0.6785-0.7122-0.4840.27120.45290.49750.19691.9540.5926-0.18041.5722-0.14530.9667-2.8543-13.0547-73.2289
54.38771.6084-1.18114.27260.61252.49030.13220.544-0.743-0.8882-0.27460.34850.8859-0.07710.07231.58620.2077-0.14211.0191-0.14660.9099-5.2245-17.0846-49.8852
60.31060.7555-0.46342.4378-0.05782.76970.04490.18830.1672-0.216-0.04860.4541-0.3816-0.3397-0.56760.0942-0.15270.24660.6001-0.0340.6598-34.900522.6295-52.7962
71.7406-1.23530.35713.2729-1.02630.3154-0.04980.8454-0.2444-1.0864-0.131-0.4310.04760.76530.29021.29270.19510.07981.2162-0.07820.8388-0.71150.9903-53.2876
83.01541.0184-0.78216.3254-0.63885.6790.16860.0560.16720.39850.20410.0263-0.163-0.299-0.23531.1301-0.0064-0.21960.54640.09750.728-38.032542.6379-68.3371
92.3237-2.57250.47512.9811-1.11863.3569-0.5533-0.45870.59030.38960.0905-0.7774-0.05050.76780.62081.4965-0.2631-0.10011.65530.26651.81634.609943.5832-51.7082
100.51290.1778-0.81782.6803-1.01081.62720.1049-0.00480.66090.3903-0.6675-1.7745-0.47551.58270.53861.47360.0237-0.34872.21450.23262.804940.36688.3854-32.7937
116.0493-1.5136-2.63186.32490.15563.95880.1164-0.0604-0.1601-0.501-0.00360.0692-0.28650.357-0.1611.00090.002-0.22390.628-0.04020.4743-29.704243.5841-88.1934
124.5264-4.6366-1.94238.67642.98772.34920.3241-0.70780.44360.3710.06970.19430.0976-0.1998-0.42391.77980.0843-0.02411.22470.00081.1042-41.285876.1477-60.2693
134.3160.13580.30634.70410.28083.297-0.2831-0.4510.32430.64120.2892-0.1112-0.9398-0.56260.08310.790.1649-0.0580.38-0.02590.5681-39.788112.0032-22.8169
144.0986-0.52480.82544.2181-0.89613.4302-0.2609-0.79770.40040.4980.0524-0.0769-0.85350.01570.41041.30910.1943-0.18120.913-0.05060.7629-15.3978-7.6438-0.5339
153.04910.39481.69621.17921.24822.43260.1158-0.3892-0.36040.1647-0.00250.41170.305-0.3128-0.04041.51190.1672-0.23461.0940.26661.0497-28.7636-42.3626.1465
166.29460.7512-0.40362.90311.86263.63770.4331-0.4165-0.19850.35050.01690.14030.4514-0.2771-0.24930.9053-0.183-0.09220.62150.16550.6322-52.4063-27.8153-18.3844
175.4278-2.09010.21696.41370.55144.73830.463-0.0295-0.344-0.8642-0.06590.32730.558-0.0201-0.48050.7609-0.0533-0.0150.5335-0.00640.5081-42.6461-10.0941-30.6996
182.3475-0.84581.13662.9052-1.48821.21320.17630.23970.05-0.325-0.1163-0.33730.59970.3972-0.02651.53440.2036-0.17181.033-0.02870.7585-1.1797-26.7792-10.1103
193.4468-1.32961.33491.585-1.21840.9698-0.461-1.0174-0.10871.32820.43630.06510.1937-0.29270.00061.2102-0.0065-0.18380.70850.04070.7851-36.972-8.8505-12.8333
204.41030.02260.28752.98680.45492.8120.14540.2428-0.06730.0937-0.380.13120.32880.3240.30341.53920.3263-0.44870.93810.07730.99025.0904-39.284611.5687
213.20771.53281.65732.19060.54560.8931-0.77160.56260.30850.53320.30580.1322-0.9714-0.04980.49392.06430.3214-0.291.9932-0.24441.2506-15.5126-0.232323.2213
223.5857-0.31521.2393.68511.26965.172-0.1961-1.19290.58920.19450.1223-0.1035-0.1442-0.56950.01640.9690.3917-0.0441.3708-0.3170.848-50.553934.2321.6694
236.28551.3499-0.31820.95370.00563.581-0.0277-0.6824-0.37930.01710.19580.42640.1938-0.6982-0.26011.73840.1223-0.37521.13150.17441.0436-9.6188-50.377823.3247
242.920.5713-1.34194.51050.90712.1559-0.30290.03770.2148-0.8820.1687-0.4161-0.31481.16390.02921.5469-0.0918-0.38441.68740.17191.161227.9982-33.675438.5109
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1resid 20:139 and chain AA20 - 139
2X-RAY DIFFRACTION2(resid 140:236 or resid 1801) and chain AA140 - 236
3X-RAY DIFFRACTION2(resid 140:236 or resid 1801) and chain AA1801
4X-RAY DIFFRACTION3resid 237:361 and chain AA237 - 361
5X-RAY DIFFRACTION4resid 362:468 and chain AA362 - 468
6X-RAY DIFFRACTION5resid 469:568 and chain AA469 - 568
7X-RAY DIFFRACTION6(chain A and resid 569:605) or (chain B and resid 757:831)A569 - 605
8X-RAY DIFFRACTION6(chain A and resid 569:605) or (chain B and resid 757:831)B757 - 831
9X-RAY DIFFRACTION7resid 606:670 and chain AA606 - 670
10X-RAY DIFFRACTION8(resid 832:934 or resid 1802) and chain BB832 - 934
11X-RAY DIFFRACTION8(resid 832:934 or resid 1802) and chain BB1802
12X-RAY DIFFRACTION9(resid 935:982 or resid 1321:1392) and chain BB935 - 982
13X-RAY DIFFRACTION9(resid 935:982 or resid 1321:1392) and chain BB1321 - 1392
14X-RAY DIFFRACTION10resid 983:1320 and chain BB983 - 1320
15X-RAY DIFFRACTION11(chain B and resid 1393:1413) or (chain C and resid 1464:1579)B1393 - 1413
16X-RAY DIFFRACTION11(chain B and resid 1393:1413) or (chain C and resid 1464:1579)C1464 - 1579
17X-RAY DIFFRACTION12resid 1580:1744 and chain CC1580 - 1744
18X-RAY DIFFRACTION13resid 20:139 and chain DD20 - 139
19X-RAY DIFFRACTION14(resid 140:236 or resid 1801) and chain DD140 - 236
20X-RAY DIFFRACTION14(resid 140:236 or resid 1801) and chain DD1801
21X-RAY DIFFRACTION15resid 237:361 and chain DD237 - 361
22X-RAY DIFFRACTION16resid 362:468 and chain DD362 - 468
23X-RAY DIFFRACTION17resid 469:568 and chain DD469 - 568
24X-RAY DIFFRACTION18(chain D and resid 569:605) or (chain E and resid 757:831)D569 - 605
25X-RAY DIFFRACTION18(chain D and resid 569:605) or (chain E and resid 757:831)E757 - 831
26X-RAY DIFFRACTION19resid 606:670 and chain DD606 - 670
27X-RAY DIFFRACTION20(resid 832:934 or resid 1802) and chain EE832 - 934
28X-RAY DIFFRACTION20(resid 832:934 or resid 1802) and chain EE1802
29X-RAY DIFFRACTION21(resid 935:982 or resid 1321:1392) and chain EE935 - 982
30X-RAY DIFFRACTION21(resid 935:982 or resid 1321:1392) and chain EE1321 - 1392
31X-RAY DIFFRACTION22resid 983:1320 and chain EE983 - 1320
32X-RAY DIFFRACTION23(chain E and resid 1393:1413) or (chain F and resid 1464:1579)E1393 - 1413
33X-RAY DIFFRACTION23(chain E and resid 1393:1413) or (chain F and resid 1464:1579)F1464 - 1579
34X-RAY DIFFRACTION24resid 1580:1750 and chain FF1580 - 1750

+
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