[English] 日本語
Yorodumi
- PDB-7ad7: Crystal structure of human complement C5 in complex with the K8 b... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7ad7
TitleCrystal structure of human complement C5 in complex with the K8 bovine knob domain peptide.
Components
  • Complement C5Complement component 5
  • K8 peptide
KeywordsIMMUNE SYSTEM / Complement C5 / C5 / ultralong / ultra-long / knob domain.
Function / homology
Function and homology information


Terminal pathway of complement / membrane attack complex / Activation of C3 and C5 / negative regulation of macrophage chemotaxis / complement activation, alternative pathway / chemokine activity / endopeptidase inhibitor activity / positive regulation of vascular endothelial growth factor production / positive regulation of chemokine production / complement activation, classical pathway ...Terminal pathway of complement / membrane attack complex / Activation of C3 and C5 / negative regulation of macrophage chemotaxis / complement activation, alternative pathway / chemokine activity / endopeptidase inhibitor activity / positive regulation of vascular endothelial growth factor production / positive regulation of chemokine production / complement activation, classical pathway / Peptide ligand-binding receptors / Regulation of Complement cascade / chemotaxis / G alpha (i) signalling events / killing of cells of another organism / cell surface receptor signaling pathway / inflammatory response / G protein-coupled receptor signaling pathway / signaling receptor binding / extracellular space / extracellular exosome / extracellular region
Similarity search - Function
: / Complement component 5, CUB domain / Complement C3/4/5, macroglobulin domain MG1 / Macroglobulin domain MG1 / Anaphylatoxin, complement system domain / Anaphylatoxin domain signature. / Anaphylatoxin/fibulin / Anaphylatoxin, complement system / Anaphylotoxin-like domain / Anaphylatoxin domain profile. ...: / Complement component 5, CUB domain / Complement C3/4/5, macroglobulin domain MG1 / Macroglobulin domain MG1 / Anaphylatoxin, complement system domain / Anaphylatoxin domain signature. / Anaphylatoxin/fibulin / Anaphylatoxin, complement system / Anaphylotoxin-like domain / Anaphylatoxin domain profile. / Anaphylatoxin homologous domain / Netrin C-terminal Domain / Netrin module, non-TIMP type / UNC-6/NTR/C345C module / Alpha-macroglobulin, receptor-binding / Alpha-macroglobulin, receptor-binding domain superfamily / Macroglobulin domain MG4 / Macroglobulin domain MG3 / A-macroglobulin receptor binding domain / Macroglobulin domain MG4 / Macroglobulin domain MG3 / A-macroglobulin receptor / Netrin domain / NTR domain profile. / Tissue inhibitor of metalloproteinases-like, OB-fold / Alpha-2-macroglobulin / Macroglobulin domain / 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 / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid / Immunoglobulin-like fold
Similarity search - Domain/homology
CYSTEINE / ETHANOL / (CARBAMOYLMETHYL-CARBOXYMETHYL-AMINO)-ACETIC ACID / Complement C5
Similarity search - Component
Biological speciesHomo sapiens (human)
Bos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsMacpherson, A. / van den Elsen, J.M.H. / Schulze, M.E. / Birtley, J.R.
CitationJournal: Elife / Year: 2021
Title: The allosteric modulation of Complement C5 by knob domain peptides.
Authors: Macpherson, A. / Laabei, M. / Ahdash, Z. / Graewert, M.A. / Birtley, J.R. / Schulze, M.E. / Crennell, S. / Robinson, S.A. / Holmes, B. / Oleinikovas, V. / Nilsson, P.H. / Snowden, J. / ...Authors: Macpherson, A. / Laabei, M. / Ahdash, Z. / Graewert, M.A. / Birtley, J.R. / Schulze, M.E. / Crennell, S. / Robinson, S.A. / Holmes, B. / Oleinikovas, V. / Nilsson, P.H. / Snowden, J. / Ellis, V. / Mollnes, T.E. / Deane, C.M. / Svergun, D. / Lawson, A.D. / van den Elsen, J.M.
History
DepositionSep 14, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 10, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 7, 2021Group: Structure summary / Category: audit_author
Revision 1.2Jan 31, 2024Group: 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Complement C5
A: Complement C5
C: K8 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)384,30513
Polymers382,9863
Non-polymers1,32010
Water7,242402
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS, 1:1 COMPLEX BETWEEN CHAINS A AND B AND THE PEPTIDE (chain C)., gel filtration, As part of a SEC MALLS experiment, the complex agreed with a A,B and C complex.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11340 Å2
ΔGint-41 kcal/mol
Surface area67690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.559, 161.695, 187.380
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

-
Protein , 2 types, 3 molecules BAC

#1: Protein Complement C5 / Complement component 5 / C3 and PZP-like alpha-2-macroglobulin domain-containing protein 4


Mass: 188512.094 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: C5, CPAMD4 / Production host: Homo sapiens (human) / References: UniProt: P01031
#2: Protein K8 peptide


Mass: 5961.453 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)

-
Sugars , 1 types, 1 molecules

#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE

-
Non-polymers , 6 types, 411 molecules

#4: Chemical
ChemComp-EOH / ETHANOL / Ethanol


Mass: 46.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-MHA / (CARBAMOYLMETHYL-CARBOXYMETHYL-AMINO)-ACETIC ACID / N-(2-ACETAMIDO)IMINODIACETIC ACID / ADA (buffer)


Mass: 190.154 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H10N2O5 / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#6: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#7: Chemical ChemComp-CYS / CYSTEINE / Cysteine


Type: L-peptide linking / Mass: 121.158 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C3H7NO2S / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-TAM / TRIS(HYDROXYETHYL)AMINOMETHANE / Tris


Mass: 163.215 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H17NO3 / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 402 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.61 Å3/Da / Density % sol: 23.75 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / Details: 0.1M ADA, 14% ethanol.

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 28, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.3→93.69 Å / Num. obs: 171135 / % possible obs: 99.83 % / Redundancy: 2 % / Biso Wilson estimate: 46.65 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.04257 / Net I/σ(I): 13.17
Reflection shellResolution: 2.3→2.382 Å / Rmerge(I) obs: 0.3613 / Mean I/σ(I) obs: 2.07 / Num. unique obs: 10933 / CC1/2: 0.668 / % possible all: 99.82

-
Processing

Software
NameVersionClassification
REFMAC5.5refinement
PHENIX1.18_3845refinement
xia2data reduction
Aimlessdata scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3CU7

3cu7


Resolution: 2.3→93.69 Å / SU ML: 0.2806 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.1592
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2336 5585 5.05 %
Rwork0.202 104905 -
obs0.2036 171135 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 65.09 Å2
Refinement stepCycle: LAST / Resolution: 2.3→93.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11568 0 86 402 12056
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003211954
X-RAY DIFFRACTIONf_angle_d0.627116228
X-RAY DIFFRACTIONf_chiral_restr0.0471841
X-RAY DIFFRACTIONf_plane_restr0.00362061
X-RAY DIFFRACTIONf_dihedral_angle_d17.40264357
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.330.37251700.30113487X-RAY DIFFRACTION99.89
2.33-2.350.34261770.29713435X-RAY DIFFRACTION99.67
2.35-2.380.29951780.27553465X-RAY DIFFRACTION99.89
2.38-2.410.30061650.27563520X-RAY DIFFRACTION99.81
2.41-2.440.28671590.2663436X-RAY DIFFRACTION99.69
2.44-2.480.30151940.26853448X-RAY DIFFRACTION99.78
2.48-2.510.30511700.26813448X-RAY DIFFRACTION99.61
2.51-2.550.31052080.27033478X-RAY DIFFRACTION99.78
2.55-2.590.34171730.27613417X-RAY DIFFRACTION99.72
2.59-2.630.30861820.26263508X-RAY DIFFRACTION99.81
2.63-2.680.30262060.25883395X-RAY DIFFRACTION99.92
2.68-2.730.2731920.25013486X-RAY DIFFRACTION99.84
2.73-2.780.31021830.24613454X-RAY DIFFRACTION99.73
2.78-2.840.24842180.22943453X-RAY DIFFRACTION99.86
2.84-2.90.27531940.2233461X-RAY DIFFRACTION99.89
2.9-2.970.28481660.22913497X-RAY DIFFRACTION99.78
2.97-3.040.28121860.22393474X-RAY DIFFRACTION99.89
3.04-3.120.2772070.23663466X-RAY DIFFRACTION99.95
3.12-3.210.27791860.23063486X-RAY DIFFRACTION99.97
3.21-3.320.23582060.21513460X-RAY DIFFRACTION100
3.32-3.440.22531800.20323534X-RAY DIFFRACTION99.97
3.44-3.570.21061660.19173514X-RAY DIFFRACTION99.92
3.57-3.740.24351890.18823487X-RAY DIFFRACTION99.86
3.74-3.930.20371800.18593543X-RAY DIFFRACTION99.97
3.93-4.180.20831980.17413514X-RAY DIFFRACTION100
4.18-4.50.18491720.15333568X-RAY DIFFRACTION99.97
4.5-4.950.17192130.14883510X-RAY DIFFRACTION99.97
4.96-5.670.20161780.16013586X-RAY DIFFRACTION99.97
5.67-7.150.20982050.19043592X-RAY DIFFRACTION99.95
7.15-93.690.20391840.19783783X-RAY DIFFRACTION99.4
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)
19.445470997011.30105772027-6.1072814436.51757796028-1.389545020178.792261219980.2013151085261.179916379830.426720077601-0.3462821492520.09895967793270.288376994111-0.182307744655-0.501782736269-0.3358858162610.3580884384330.01115028724150.006324550869850.3408174393420.104927703610.27984659862746.791391745245.01142726640.802376776006
21.909558923210.588798224616-0.3079096094522.2885499074-2.222788444022.214418010930.3038354832940.157147763049-0.5091063750990.0252580530325-0.08467661497430.614355522204-0.0109960197219-0.334152950885-0.1948545463490.778091936176-0.0949185151337-0.2928776492150.995823903310.2338867676251.0741467259832.480946894452.4275144829-7.5172212484
37.43157271495-3.485907915051.682671865494.606481182974.312108774959.138583448980.21097835524-1.376758337051.37773427421-1.796162631020.07123125421332.00398951009-0.820418760028-1.70350719717-0.293345883580.7716623671060.3148403568210.03657692750081.51579904249-0.1450484301331.3651992838938.647206975753.920165389-13.7469563347
41.99998730742-8.331400015667.155164389117.12849800265-1.443911418186.019713528680.7160624288421.691690865611.71908616533-0.574705079579-0.8384854775920.1133335987050.09888643334410.9524411592340.1265799982261.52550631039-0.05633458877930.0629248817441.56815775746-0.1828249898351.5364037790154.806683613953.620014100328.8300495064
55.118981980830.8671915948621.173002004793.97155781180.1053020119945.146056280970.219961217638-0.1403157399370.1144452001170.0477080495919-0.1550617227870.0926311921427-0.0365428884814-0.393520005443-0.04597317677370.217326894644-0.006301234641610.06459876853970.373092600652-0.009109024640240.3206027255628.451094973545.694775280791.8224188665
61.92420551345-0.847238419357-0.6129084641661.68080411702-0.02105558233392.57173227847-0.1110405328610.228568156947-0.12991402044-0.1600790389030.03536142308760.07490797449890.2355365296040.05895866790830.06372146565480.350218334117-0.06357667275730.008664411752570.567683868321-0.1000443804710.29663577876140.628308447836.878631769957.8500882139
71.571760714612.39019247940.9807142990593.911915648972.61770667143.63788644822-0.4263095165810.944948584886-0.127775022331-0.819114676750.870928271114-0.450075197015-0.2121023011720.937168958003-0.3863502393510.789294109972-0.0270602808430.1923531767761.03620324709-0.2145344296390.74201694980869.051802893555.662179790944.019204286
82.472436079120.506421290987-1.340755704421.164598633851.230984005366.55607234537-0.01160464487280.198390200187-0.0866679339272-0.210933910561-0.0277109559473-0.0877711304662-0.2296229815270.330888128794-0.005275363457420.405883214616-0.01002169761790.1002287830630.280570682666-0.05393734334830.68729182399965.030965420265.901851969.3997040451
92.28409954637-0.235165921878-0.005653593814447.00392023441.740594496993.841329621260.0703155154338-0.3563255905920.4313160858170.5486374272730.035162762027-0.398778047679-0.09715014221160.261439342529-0.1147307797850.243058971957-0.0461909458205-0.004752770731880.395414302611-0.02668734198270.39069282603450.074476135752.855831620996.7067583521
102.14500031419-1.36818552854-3.114709782081.610251642323.325374185278.40595333116-0.09321663962190.07637177310.0660253208578-0.1833143737260.35444046248-0.7260353203440.5206223299131.21155355843-0.2748642354610.500491311040.1723311336670.1085104257220.845732868986-0.006678476225680.54723665273564.017824477727.11283239767.6082799606
110.1753832238290.02931573850320.02038603128160.4689291415670.5626003016391.45558821327-0.04755286325860.2214238782060.0764010529655-0.0152495496325-0.06599007428560.191825588894-0.00121766788728-0.05109585278470.1066309639230.3783628892690.007629763176330.1010314948330.5134162948560.02650259271840.50116950966646.774316768445.839830204177.4583857228
120.3152326401320.138100666384-0.234845676559-0.1836070387520.5119529523621.40054608172-0.114735319943-0.1677340831440.1391409249870.009302340887560.04166823343010.0420341602152-0.1530175950340.3791678319620.1079322016580.5129003148940.001759461642180.06670796409810.6034663069530.0201107978740.5764563367363.677039694734.296674727237.5012266303
131.792995312230.259690007585-0.2082845458370.983987361808-0.08730103945210.888918988329-0.0896456643672-0.236260077712-0.2143445918070.1213474276880.0116556412856-0.08681905082110.02414196706190.04426467766940.07847942416210.2848673116380.04059322292670.01280675531570.3275882108480.03522757426060.23961607709732.976168007626.10896139921.8015834651
144.069473781375.302686079814.085097746646.902515843075.327550493374.11667213286-0.7697808300030.8882093739760.670426382503-1.24544198960.4799863889081.74117871362-1.44286927839-0.4235973601860.2982842834970.612436320822-0.0127348074901-0.1187229923720.69050056862-0.003190208184010.612589210738.127416724450.6048812862-5.83560427668
154.57030480277-0.5015242119942.779305993350.231506837630.4882864508825.592798809420.0008955230120670.437686049512-0.04750846707050.0411058081378-0.01156132828990.141589086991-0.1401538555670.242470006672-0.01998896743710.417942439812-0.05672123392480.01551640044380.4004890156710.0002522438812650.39216196215645.232561328441.4788557265-5.23987220581
163.128893003752.236824544454.272899286772.286487366913.019059138237.50306005693-0.1115375845230.629302157545-2.09925738112-0.5396183921440.40685752143-2.15348840456-0.1104589819910.499101055912-0.3313366712180.333732743646-0.07181923470930.05033543950860.5602783031170.008903492721580.63309187876558.381052839737.21899295190.452750358342
173.24261665069-1.528250223811.230126394264.125026290993.775632330995.954306644860.006725655311920.119112994759-0.437259398372-0.5327465241310.1258807541350.7093409640130.100220334024-0.313293341873-0.1131103401370.385870031289-0.05447166147240.03173451046870.4953006743210.05413554521650.30447292748945.236472456739.3556234684-4.5045455877
185.31725726858-0.902012616226-3.005300483575.59759682147-4.818250221536.915507532720.150127032364-0.3246389290962.18926564522-0.7955771297230.02922952647290.235376318488-0.6811099591190.470259766998-0.1132517754790.583232674816-0.0976031696442-0.05049120866490.416187684417-0.02368989761780.65109759387150.273086730252.4212971987-1.12343499619
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'C' and (resid 36 through 45 )CC36 - 4537 - 47
22chain 'C' and (resid 46 through 50 )CC46 - 5048 - 52
33chain 'C' and (resid 51 through 52 )CC51 - 5253 - 54
44chain 'M' and (resid 1 through 1 )MO11
55chain 'B' and (resid 20 through 118 )BA20 - 1181 - 99
66chain 'B' and (resid 119 through 219 )BA119 - 219100 - 200
77chain 'B' and (resid 220 through 293 )BA220 - 293201 - 274
88chain 'B' and (resid 294 through 455 )BA294 - 455275 - 436
99chain 'B' and (resid 456 through 562 )BA456 - 562437 - 543
1010chain 'B' and (resid 563 through 588 )BA563 - 588544 - 571
1111chain 'B' and (resid 589 through 671 )BA589 - 671572 - 637
1212chain 'A' and (resid 683 through 929 )AB683 - 9291 - 212
1313chain 'A' and (resid 930 through 1513 )AB930 - 1513213 - 785
1414chain 'C' and (resid 1 through 6 )CC1 - 61 - 6
1515chain 'C' and (resid 7 through 15 )CC7 - 157 - 15
1616chain 'C' and (resid 16 through 22 )CC16 - 2216 - 23
1717chain 'C' and (resid 23 through 30 )CC23 - 3024 - 31
1818chain 'C' and (resid 31 through 35 )CC31 - 3532 - 36

+
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