[English] 日本語
Yorodumi
- PDB-8u32: Crystal structure of PD-1 in complex with a Fab -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8u32
TitleCrystal structure of PD-1 in complex with a Fab
Components
  • Fab heavy chain
  • Fab light chain
  • Programmed cell death protein 1
KeywordsSTRUCTURAL PROTEIN/IMMUNE SYSTEM / PD-1 / Fab / STRUCTURAL PROTEIN / STRUCTURAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


negative regulation of tolerance induction / regulatory T cell apoptotic process / B cell apoptotic process / negative regulation of immune response / positive regulation of T cell apoptotic process / negative regulation of B cell apoptotic process / humoral immune response / regulation of immune response / PD-1 signaling / adaptive immune response ...negative regulation of tolerance induction / regulatory T cell apoptotic process / B cell apoptotic process / negative regulation of immune response / positive regulation of T cell apoptotic process / negative regulation of B cell apoptotic process / humoral immune response / regulation of immune response / PD-1 signaling / adaptive immune response / Potential therapeutics for SARS / external side of plasma membrane / apoptotic process / plasma membrane
Similarity search - Function
Programmed cell death protein 1 / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Programmed cell death protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.51 Å
AuthorsSun, D. / Masureel, M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Mabs / Year: 2024
Title: Structure- and machine learning-guided engineering demonstrate that a non-canonical disulfide in an anti-PD-1 rabbit antibody does not impede antibody developability.
Authors: Liang, W.C. / Xi, H. / Sun, D. / D'Ascenzo, L. / Zarzar, J. / Stephens, N. / Cook, R. / Li, Y. / Ye, Z. / Matsumoto, M. / Payandeh, J. / Masureel, M. / Wu, Y.
History
DepositionSep 7, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Programmed cell death protein 1
B: Fab light chain
C: Fab heavy chain
D: Programmed cell death protein 1
E: Fab light chain
F: Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,0148
Polymers126,5726
Non-polymers4422
Water2,612145
1
A: Programmed cell death protein 1
B: Fab light chain
C: Fab heavy chain


Theoretical massNumber of molelcules
Total (without water)63,2863
Polymers63,2863
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Programmed cell death protein 1
E: Fab light chain
F: Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,7285
Polymers63,2863
Non-polymers4422
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.482, 88.881, 235.859
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
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 31 through 32 or resid 35...
d_2ens_1(chain "D" and (resid 31 through 32 or resid 35...
d_1ens_2(chain "B" and (resid 1 through 126 or resid 128...
d_2ens_2(chain "E" and (resid 1 through 126 or resid 128...
d_1ens_3(chain "C" and (resid 2 through 43 or resid 45...
d_2ens_3(chain "F" and (resid 2 through 43 or resid 45...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1PROPROTRPTRPAA31 - 3222 - 23
d_12ens_1PROPROSERSERAA35 - 5726 - 48
d_13ens_1SERSERPROPROAA62 - 8353 - 74
d_14ens_1SERSERPHEPHEAA93 - 9584 - 86
d_15ens_1VALVALGLYGLYAA97 - 10388 - 94
d_16ens_1ASPASPVALVALAA105 - 11196 - 102
d_17ens_1ALAALAALAALAAA113104
d_18ens_1ASNASNILEILEAA116 - 134107 - 125
d_19ens_1SERSERVALVALAA137 - 144128 - 135
d_21ens_1PROPROTRPTRPDD31 - 3222 - 23
d_22ens_1PROPROSERSERDD35 - 5726 - 48
d_23ens_1SERSERPROPRODD62 - 8353 - 74
d_24ens_1SERSERPHEPHEDD93 - 9584 - 86
d_25ens_1VALVALGLYGLYDD97 - 10388 - 94
d_26ens_1ASPASPVALVALDD105 - 11196 - 102
d_27ens_1ALAALAALAALADD113104
d_28ens_1ASNASNILEILEDD116 - 134107 - 125
d_29ens_1SERSERVALVALDD137 - 144128 - 135
d_11ens_2ALAALAASPASPBB1 - 1261 - 126
d_12ens_2GLNGLNSERSERBB128 - 172128 - 172
d_13ens_2ASPASPHISHISBB174 - 202174 - 202
d_14ens_2GLYGLYGLUGLUBB204 - 217204 - 217
d_21ens_2ALAALAASPASPEE1 - 1261 - 126
d_22ens_2GLNGLNSERSEREE128 - 172128 - 172
d_23ens_2ASPASPHISHISEE174 - 202174 - 202
d_24ens_2GLYGLYGLUGLUEE204 - 217204 - 217
d_11ens_3GLNGLNGLYGLYCC2 - 432 - 43
d_12ens_3GLYGLYASPASPCC45 - 7545 - 75
d_13ens_3SERSERSERSERCC77 - 14177 - 141
d_14ens_3THRTHRHISHISCC149 - 214149 - 214
d_15ens_3PROPROLYSLYSCC216 - 223216 - 223
d_16ens_3VALVALLYSLYSCC225 - 228225 - 228
d_21ens_3GLNGLNGLYGLYFF2 - 432 - 43
d_22ens_3GLYGLYASPASPFF45 - 7545 - 75
d_23ens_3SERSERSERSERFF77 - 14177 - 141
d_24ens_3THRTHRHISHISFF149 - 214149 - 214
d_25ens_3PROPROLYSLYSFF216 - 223216 - 223
d_26ens_3VALVALLYSLYSFF225 - 228225 - 228

NCS ensembles :
ID
ens_1
ens_2
ens_3

NCS oper:
IDCodeMatrixVector
1given(-0.920933275438, 0.270580089267, 0.280478729109), (0.183470411321, -0.333939018252, 0.924566568863), (0.343832096175, 0.90292366642, 0.257892113603)-18.5921904016, -76.0092613261, 61.4333048192
2given(-0.948097711802, 0.242211369554, 0.20602034204), (0.138235573976, -0.269520554615, 0.953021299199), (0.286359310942, 0.932036653302, 0.22204959342)-18.2760581886, -76.3364824466, 61.8067083638
3given(-0.937282641878, 0.263093132276, 0.228655314792), (0.141656261, -0.3118703506, 0.93950539548), (0.318488230478, 0.912972556086, 0.255041876721)-18.5097277423, -76.6710804127, 61.0985525539

-
Components

#1: Protein Programmed cell death protein 1


Mass: 15765.327 Da / Num. of mol.: 2 / Mutation: C93S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PDCD1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15116
#2: Antibody Fab light chain


Mass: 23509.783 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#3: Antibody Fab heavy chain


Mass: 24010.879 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#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.: 2 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.17 Å3/Da / Density % sol: 61.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 20 %w/v PEG 3350, 0.2 M Na2 Malon, 0.1 M BIS-TRIS prop pH 8.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9794 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 27, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.51→84.17 Å / Num. obs: 52262 / % possible obs: 93 % / Redundancy: 6.7 % / Biso Wilson estimate: 48.32 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.077 / Net I/σ(I): 16.7
Reflection shellResolution: 2.51→2.6 Å / Rmerge(I) obs: 0.6855 / Num. unique obs: 5506 / CC1/2: 0.884 / % possible all: 99.6

-
Processing

Software
NameVersionClassification
PHENIX1.18.2-3874_finalrefinement
autoPROCdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.51→34.96 Å / SU ML: 0.3163 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.6325
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2304 2663 5.1 %
Rwork0.1954 49552 -
obs0.1972 52215 93.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 61.37 Å2
Refinement stepCycle: LAST / Resolution: 2.51→34.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8366 0 28 145 8539
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0098585
X-RAY DIFFRACTIONf_angle_d1.22211678
X-RAY DIFFRACTIONf_chiral_restr0.06751320
X-RAY DIFFRACTIONf_plane_restr0.00831502
X-RAY DIFFRACTIONf_dihedral_angle_d34.16591194
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS0.835179540219
ens_2d_2BBX-RAY DIFFRACTIONTorsion NCS1.06956829943
ens_3d_2CCX-RAY DIFFRACTIONTorsion NCS0.714262952636
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.51-2.550.35521390.29632779X-RAY DIFFRACTION99.39
2.55-2.60.32491340.26792755X-RAY DIFFRACTION99.9
2.6-2.650.3211290.26922575X-RAY DIFFRACTION97.37
2.69-2.710.2675610.26071184X-RAY DIFFRACTION97.11
2.71-2.770.3041540.24632752X-RAY DIFFRACTION99.79
2.77-2.840.27041630.24182745X-RAY DIFFRACTION99.35
2.84-2.920.26481630.23972735X-RAY DIFFRACTION99.93
2.92-3.010.30991510.24182778X-RAY DIFFRACTION99.97
3.01-3.10.27561550.24422772X-RAY DIFFRACTION99.93
3.1-3.210.27011470.2412727X-RAY DIFFRACTION97.82
3.21-3.340.26291440.23492729X-RAY DIFFRACTION97.75
3.34-3.50.2962620.23051193X-RAY DIFFRACTION42.86
3.5-3.680.26751550.21442793X-RAY DIFFRACTION99.76
3.68-3.910.20441530.18982796X-RAY DIFFRACTION99.66
3.91-4.210.22671470.17232831X-RAY DIFFRACTION99.73
4.21-4.630.16361400.13952803X-RAY DIFFRACTION99.76
4.63-5.30.15991550.14462765X-RAY DIFFRACTION97.24
5.3-6.670.22941530.17422873X-RAY DIFFRACTION99.64
6.67-34.960.18361580.16762967X-RAY DIFFRACTION97.93
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)
14.04269176096-1.08918249741-0.8064197064620.719174740395-0.9071095114195.49255699943-0.09314319481480.326943536176-0.375168403707-0.5202280095520.0666123478640.01988379239580.351821766705-0.2414534656580.01273166439760.4609988546490.0205774931396-0.03013554325680.381027971792-0.03589196662030.360337942118-22.1797842575-30.12785337468.98377461887
22.982507962460.9357189009530.1788833175521.69236934215-1.153875844333.4866852396-0.0805601350220.00926153230210.040106722117-0.2647799592510.04709564408870.403547738973-0.0156690941433-0.0777400453730.04255400806730.4075457551950.0595694157132-0.04068855936150.359566409213-0.05112744032040.369479674994-25.0165840615-23.658397105410.2030569181
31.652435761870.629012563662-0.177274457010.210196799729-0.01438833258390.843314715835-0.148078596703-0.0187390299954-0.113765401214-0.07474984843410.131727307666-0.1397594469880.006667278898610.1502508959550.01471634351290.5158613377380.02799284319570.009260254849620.36925187406-0.03497756753470.3864589298693.2374782093-10.915278123213.8932995158
44.92367141767-0.3982608914823.975754985251.06831560641-0.04876456688318.01191319663-0.05144166701650.4566354591470.130742776264-0.200680374050.137588599304-0.2795662929950.3534629021520.913165047565-0.1764648845120.404838856285-0.006412596547930.06842240148990.341978459303-0.04611216144910.45250204915114.4124176064-10.654967052313.8389016016
55.379562641731.678136668840.4034902296327.19310488127-2.74130892437.659882919580.002306606910970.0610672876964-0.112563008691-0.4936204360450.206543737887-0.2101398816070.378337345502-0.342752082162-0.2053971188370.344343830114-0.05296630771550.08530477195670.382993684420.003848535903090.4294934328129.38420517068-47.170161291310.7596486347
63.0622041004-1.058033847185.126356083571.85434078929-2.065516832868.640073720820.6772203207960.220522332817-1.364973741840.003020354818510.6723100638570.3808295193071.02202072426-0.957441743214-1.373394615931.07598467768-0.366497877987-0.1194879566740.769681163073-0.095785161690.9196106679855.10708029634-58.71847040424.64417310694
74.056634314140.797759690318-0.9584659789926.01104035709-3.62807684087.47182612684-0.03559218902910.8358315831150.0280927413525-0.8113330873390.224134943225-0.02482906658540.556721729893-0.0856912897766-0.09163008874410.459349288991-0.1208704038840.08941726335420.534143220926-0.06148486215370.4925233865159.46045781607-49.55042313734.45900671922
80.4876317302810.727413773532-1.119890309162.69392001973-2.139026154513.64561145024-0.1042527730080.05770766787340.02785355438910.1820885827650.3661831342960.22648130587-0.532131215281-0.437540733105-0.1908240047620.3499205335540.001159852989780.001303111903250.4390027501850.06390681453950.5649844158678.46286862699-45.030673358112.2455711853
96.18294065669-3.44080116702-2.358321985445.190144600362.768781766972.96976358321-0.236358808443-0.267736925983-0.001245945625610.6546816311870.331997401202-0.3654079716180.1075763810480.298170102584-0.1099168506390.467715639772-0.0182560447622-0.1088250025630.3068393525120.03103569807440.3457379637482.86446231465-44.266072202641.5679487422
102.065782308380.46799467339-1.045601724044.75619177681-1.72632291555.869449953580.0524758739257-0.0603709450295-0.178057024545-0.453134703786-0.06077339987270.1514571568780.483450284901-0.395848660745-0.02065881443390.415003458069-0.00971974829808-0.06366874108440.4170517490330.02668438793770.369761031558-17.3642421913-53.392382081870.6724420178
115.76932684862.33563117027-1.813858540262.911131128130.257904390345.344990416040.18056163288-0.352707089554-0.5434642091850.8731849976790.2138378317621.088912585760.669397252264-0.767020745048-0.4826153722730.695896037405-0.104095221180.07643973539640.287072478814-0.06133360183360.580114001877-9.74528332584-67.64379617236.9624374423
122.41728562440.753963613199-1.113590798594.845503331270.1944343075773.38491725205-0.202002132908-0.0581381460708-0.1291120980530.5249891521910.1114874088350.1222311848190.460759790937-0.01518359633380.09301733685620.426831290182-0.00317681130524-0.003166476052660.284331554850.01846170612650.438146341741-1.00944402943-62.654877678933.279289187
132.69513732906-1.50967208821-0.09008188849874.94119434033-0.3859170789222.238505248210.2536060382680.342291255383-0.271481253756-1.26486307456-0.3118305215770.9452124686810.461142993946-0.939803330890.1104328668470.932495440368-0.104646669649-0.319086324470.7741625528960.0228191035880.67016463453-26.8601431928-59.865247892858.6006965007
144.54131802192.97146373254-2.091635142816.65859995480.9329999567597.687826655170.132144689848-0.341286959009-1.235405611560.356729143121-0.245235123077-0.6326294226550.984471429986-0.318430583619-0.004671738900170.637652401043-0.14021918401-0.1570200401110.6065167568160.1645229689660.977340646102-38.0711043535-48.606660956821.1227299243
153.890134733292.579309511341.234167148444.05810375548-0.2056236657114.903649934650.4184715763890.0497677380319-1.504067885530.2478559419620.0259047099251-0.2914752959471.32312817363-0.440634836522-0.4499323086780.690285684977-0.0901700603963-0.1119142410950.6435854136140.08170801970590.914033667512-38.995080065-49.672640463318.4364701985
167.69776045731-0.3771753681662.79125605891.406883093530.1444025828273.468197602990.0298521298471-0.1055742508550.06393144038530.1335469958490.009008289058130.153280260751-0.244489278766-0.39665746103-0.05975460143460.3689719468450.05386894853160.05223021014430.3220695190260.01900719261410.275501631785-21.2798897339-22.435707985230.4592198737
171.53083314831.18402516254-0.3186027639144.77104430063-2.067483066393.82537667861-0.0626456154110.0506883335910.1623775377040.02828141989830.113849071201-0.160491614174-0.2550448679860.0868969309207-0.04827295869620.335833789792-0.02169357839160.00345698038080.312791443316-0.03471444554960.3660692084434.878842468512.399189453323.9540862051
184.522290274883.2452325689-2.944404309444.7519947716-5.169480514396.341965760520.02833050529410.293920116684-0.247397538018-1.94481492104-0.274517086204-0.8043176498931.303407059720.6141891434210.2069644584770.5140507451840.005706145102-0.09655591416010.452233785678-0.1164852571570.246962723331-14.6984838544-22.69322031734.20654655962
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'C' and (resid 18 through 40 )CC18 - 4018 - 40
22chain 'C' and (resid 41 through 113 )CC41 - 11341 - 113
33chain 'C' and (resid 114 through 189 )CC114 - 189114 - 189
44chain 'C' and (resid 190 through 229 )CC190 - 229190 - 229
55chain 'D' and (resid 29 through 81 )DD29 - 811 - 53
66chain 'D' and (resid 82 through 94 )DD82 - 9454 - 60
77chain 'D' and (resid 95 through 127 )DD95 - 12761 - 93
88chain 'D' and (resid 128 through 147 )DD128 - 14794 - 113
99chain 'E' and (resid 1 through 110 )EG1 - 1101 - 110
1010chain 'E' and (resid 111 through 217 )EG111 - 217111 - 217
1111chain 'F' and (resid 1 through 17 )FH1 - 171 - 17
1212chain 'F' and (resid 18 through 125 )FH18 - 12518 - 125
1313chain 'F' and (resid 126 through 228 )FH126 - 228126 - 222
1414chain 'A' and (resid 31 through 81 )AA31 - 811 - 51
1515chain 'A' and (resid 82 through 144 )AA82 - 14452 - 106
1616chain 'B' and (resid 1 through 110 )BB1 - 1101 - 110
1717chain 'B' and (resid 111 through 218 )BB111 - 218111 - 218
1818chain 'C' and (resid 1 through 17 )CC1 - 171 - 17

+
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://pdbjlvh1.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