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- PDB-9l8p: in situ structure of mtHsp60-Hsp10 -

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Basic information

Entry
Database: PDB / ID: 9l8p
Titlein situ structure of mtHsp60-Hsp10
Components
  • 10 kDa heat shock protein, mitochondrial
  • 60 kDa heat shock protein, mitochondrial
KeywordsCHAPERONE / mtHsp60-Hsp10
Function / homology
Function and homology information


coated vesicle / isotype switching to IgG isotypes / mitochondrial unfolded protein response / TFAP2A acts as a transcriptional repressor during retinoic acid induced cell differentiation / apolipoprotein A-I binding / lipopolysaccharide receptor complex / protein import into mitochondrial intermembrane space / high-density lipoprotein particle binding / migrasome / cysteine-type endopeptidase activator activity ...coated vesicle / isotype switching to IgG isotypes / mitochondrial unfolded protein response / TFAP2A acts as a transcriptional repressor during retinoic acid induced cell differentiation / apolipoprotein A-I binding / lipopolysaccharide receptor complex / protein import into mitochondrial intermembrane space / high-density lipoprotein particle binding / migrasome / cysteine-type endopeptidase activator activity / positive regulation of T cell mediated immune response to tumor cell / chaperonin ATPase / Mitochondrial protein import / positive regulation of macrophage activation / negative regulation of execution phase of apoptosis / cellular response to interleukin-7 / MyD88-dependent toll-like receptor signaling pathway / biological process involved in interaction with symbiont / 'de novo' protein folding / sperm plasma membrane / apoptotic mitochondrial changes / B cell activation / B cell proliferation / : / positive regulation of interferon-alpha production / positive regulation of interleukin-10 production / DNA replication origin binding / apolipoprotein binding / RHOG GTPase cycle / positive regulation of execution phase of apoptosis / response to unfolded protein / Mitochondrial unfolded protein response (UPRmt) / isomerase activity / chaperone-mediated protein complex assembly / sperm midpiece / clathrin-coated pit / positive regulation of interleukin-12 production / protein folding chaperone / Mitochondrial protein degradation / intrinsic apoptotic signaling pathway / response to cold / T cell activation / secretory granule / protein maturation / lipopolysaccharide binding / ATP-dependent protein folding chaperone / positive regulation of T cell activation / positive regulation of interleukin-6 production / positive regulation of type II interferon production / osteoblast differentiation / p53 binding / unfolded protein binding / protein folding / single-stranded DNA binding / double-stranded RNA binding / protein-folding chaperone binding / protein refolding / early endosome / mitochondrial inner membrane / protein stabilization / mitochondrial matrix / ubiquitin protein ligase binding / negative regulation of apoptotic process / enzyme binding / cell surface / protein-containing complex / ATP hydrolysis activity / mitochondrion / extracellular space / RNA binding / extracellular exosome / ATP binding / metal ion binding / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Chaperonin GroES, conserved site / Chaperonins cpn10 signature. / Chaperonin 10 Kd subunit / GroES chaperonin family / GroES chaperonin superfamily / Chaperonin 10 Kd subunit / Chaperonin Cpn60, conserved site / Chaperonins cpn60 signature. / Chaperonin Cpn60/GroEL / GroEL-like equatorial domain superfamily ...Chaperonin GroES, conserved site / Chaperonins cpn10 signature. / Chaperonin 10 Kd subunit / GroES chaperonin family / GroES chaperonin superfamily / Chaperonin 10 Kd subunit / Chaperonin Cpn60, conserved site / Chaperonins cpn60 signature. / Chaperonin Cpn60/GroEL / GroEL-like equatorial domain superfamily / TCP-1-like chaperonin intermediate domain superfamily / GroEL-like apical domain superfamily / TCP-1/cpn60 chaperonin family / Chaperonin Cpn60/GroEL/TCP-1 family / GroES-like superfamily
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / : / 60 kDa heat shock protein, mitochondrial / 10 kDa heat shock protein, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 7.3 Å
AuthorsJung, M. / Roh, S.
Funding support Korea, Republic Of, 5items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)2019R1C1C1004598 Korea, Republic Of
National Research Foundation (NRF, Korea)2020R1A5A1018081 Korea, Republic Of
National Research Foundation (NRF, Korea)2021M3A9I4021220 Korea, Republic Of
National Research Foundation (NRF, Korea)2019M3E5D6063871 Korea, Republic Of
National Research Foundation (NRF, Korea)2020R1A6C101A183 Korea, Republic Of
CitationJournal: To Be Published
Title: In situ characterization of mtHsp60-Hsp10 chaperone complex under folding stress
Authors: Jung, M. / Roh, S.
History
DepositionDec 27, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 1, 2025Provider: repository / Type: Initial release
Revision 1.1Oct 15, 2025Group: Database references / Category: citation / Item: _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 60 kDa heat shock protein, mitochondrial
G: 60 kDa heat shock protein, mitochondrial
F: 60 kDa heat shock protein, mitochondrial
E: 60 kDa heat shock protein, mitochondrial
D: 60 kDa heat shock protein, mitochondrial
C: 60 kDa heat shock protein, mitochondrial
B: 60 kDa heat shock protein, mitochondrial
J: 60 kDa heat shock protein, mitochondrial
I: 60 kDa heat shock protein, mitochondrial
H: 60 kDa heat shock protein, mitochondrial
N: 60 kDa heat shock protein, mitochondrial
Y: 60 kDa heat shock protein, mitochondrial
L: 60 kDa heat shock protein, mitochondrial
K: 60 kDa heat shock protein, mitochondrial
O: 10 kDa heat shock protein, mitochondrial
U: 10 kDa heat shock protein, mitochondrial
T: 10 kDa heat shock protein, mitochondrial
S: 10 kDa heat shock protein, mitochondrial
R: 10 kDa heat shock protein, mitochondrial
Q: 10 kDa heat shock protein, mitochondrial
P: 10 kDa heat shock protein, mitochondrial
X: 10 kDa heat shock protein, mitochondrial
W: 10 kDa heat shock protein, mitochondrial
V: 10 kDa heat shock protein, mitochondrial
2: 10 kDa heat shock protein, mitochondrial
1: 10 kDa heat shock protein, mitochondrial
Z: 10 kDa heat shock protein, mitochondrial
M: 10 kDa heat shock protein, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,016,75756
Polymers1,009,10928
Non-polymers7,64828
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "Q"
d_2ens_1chain "2"
d_3ens_1chain "M"
d_4ens_1chain "O"
d_5ens_1chain "P"
d_6ens_1chain "1"
d_7ens_1chain "R"
d_8ens_1chain "S"
d_9ens_1chain "T"
d_10ens_1chain "U"
d_11ens_1chain "V"
d_12ens_1chain "W"
d_13ens_1chain "X"
d_14ens_1chain "Z"
d_1ens_2chain "F"
d_2ens_2chain "B"
d_3ens_2chain "C"
d_4ens_2chain "D"
d_5ens_2chain "E"
d_6ens_2chain "A"
d_7ens_2chain "G"
d_8ens_2chain "H"
d_9ens_2chain "I"
d_10ens_2chain "J"
d_11ens_2chain "K"
d_12ens_2chain "L"
d_13ens_2chain "N"
d_14ens_2chain "Y"

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_1GLYGLYASPASPQT3 - 1023 - 102
d_21ens_1GLYGLYASPASP2Y3 - 1023 - 102
d_31ens_1GLYGLYASPASPMBA3 - 1023 - 102
d_41ens_1GLYGLYASPASPOO3 - 1023 - 102
d_51ens_1GLYGLYASPASPPU3 - 1023 - 102
d_61ens_1GLYGLYASPASP1Z3 - 1023 - 102
d_71ens_1GLYGLYASPASPRS3 - 1023 - 102
d_81ens_1GLYGLYASPASPSR3 - 1023 - 102
d_91ens_1GLYGLYASPASPTQ3 - 1023 - 102
d_101ens_1GLYGLYASPASPUP3 - 1023 - 102
d_111ens_1GLYGLYASPASPVX3 - 1023 - 102
d_121ens_1GLYGLYASPASPWW3 - 1023 - 102
d_131ens_1GLYGLYASPASPXV3 - 1023 - 102
d_141ens_1GLYGLYASPASPZAA3 - 1023 - 102
d_11ens_2TYRTYRGLUGLUFC0 - 52626 - 552
d_12ens_2ATPATPATPATPFGA601
d_22ens_2ATPATPATPATPBOA601
d_31ens_2TYRTYRGLUGLUCF0 - 52626 - 552
d_32ens_2ATPATPATPATPCMA601
d_41ens_2TYRTYRGLUGLUDE0 - 52626 - 552
d_42ens_2ATPATPATPATPDKA601
d_51ens_2TYRTYRGLUGLUED0 - 52626 - 552
d_52ens_2ATPATPATPATPEIA601
d_61ens_2TYRTYRGLUGLUAA0 - 52626 - 552
d_62ens_2ATPATPATPATPACA601
d_71ens_2TYRTYRGLUGLUGB0 - 52626 - 552
d_72ens_2ATPATPATPATPGEA601
d_81ens_2TYRTYRGLUGLUHJ0 - 52626 - 552
d_82ens_2ATPATPATPATPHUA601
d_91ens_2TYRTYRGLUGLUII0 - 52626 - 552
d_92ens_2ATPATPATPATPISA601
d_101ens_2TYRTYRGLUGLUJH0 - 52626 - 552
d_102ens_2ATPATPATPATPJQA601
d_111ens_2TYRTYRGLUGLUKN0 - 52626 - 552
d_112ens_2ATPATPATPATPKCB601
d_121ens_2TYRTYRGLUGLULM0 - 52626 - 552
d_122ens_2ATPATPATPATPLAB601
d_131ens_2TYRTYRGLUGLUNK0 - 52626 - 552
d_132ens_2ATPATPATPATPNWA601
d_141ens_2TYRTYRGLUGLUYL0 - 52626 - 552
d_142ens_2ATPATPATPATPYYA601

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(0.618407633866, -0.785756366047, -0.0126068073778), (-0.785763269098, -0.618502329541, 0.00556356799154), (-0.0121689486985, 0.00646541326053, -0.999905053052)226.106960136, 456.254102119, 382.073079874
2given(-0.908306913846, 0.418209690248, 0.00889973264098), (0.418198721371, 0.908350104724, -0.00314907788304), (-0.00940104796249, 0.000861527597594, -0.999955438041)281.312845356, -60.9776781842, 382.558766529
3given(-0.21860799098, -0.975796512408, -0.00563139877814), (0.975765132761, -0.218536662568, -0.0111414901297), (0.00964116011701, -0.00793054135015, 0.999922074237)419.461230646, 49.4965362182, -0.305346224661
4given(0.617108657112, -0.786840740807, -0.00765205357881), (0.786877174857, 0.617065237236, 0.00740301858327), (-0.00110318036931, -0.0105896931584, 0.99994331909)225.159148278, -79.4263681775, 2.58174032926
5given(-0.206597508194, -0.978402653379, -0.00676146946975), (-0.978330000798, 0.206475490594, 0.0154363636157), (-0.0137069013942, 0.00980406269031, -0.999857990521)417.649272487, 332.718166633, 381.709822239
6given(0.606424657627, 0.795039820344, -0.0126814309059), (-0.795075108141, 0.60650255973, 0.00319647553408), (0.0102326456398, 0.00814426846753, 0.99991447827)-72.2841726444, 225.808955049, -3.64785539552
7given(-0.24903608275, 0.968487719621, -0.00354491647093), (-0.968351916177, -0.248935085869, 0.0180524087145), (0.0166010820635, 0.00792842780777, 0.999830757732)55.2215530491, 416.683524614, -5.03509176251
8given(-0.90660300737, 0.421938104809, 0.00626280592258), (-0.421980149211, -0.906561656622, -0.00887222714112), (0.00193408900692, -0.0106863675859, 0.999941028685)280.68498111, 445.257691645, 1.85605060906
9given(-0.896093084851, -0.443734481132, 0.0108117314193), (0.443595142148, -0.896131295079, -0.013116853377), (0.0155091310062, -0.00695789007031, 0.999855516873)441.854142439, 280.202267735, -1.70888926281
10given(0.999848144313, -0.00524221685873, -0.0166194908347), (-0.00551707247511, -0.999848055292, -0.016535665707), (-0.0165302820455, 0.0166248456076, -0.999725144369)5.928791227, 387.000953508, 380.908848928
11given(0.624367227753, 0.781123606622, 0.00338763724918), (0.781108480702, -0.624310498458, -0.0102928562928), (-0.00592505553025, 0.00907263433407, -0.999941288788)-78.2131043486, 163.706593029, 380.159222168
12given(-0.233579224397, 0.972337306707, 0.000952846641575), (0.972306772593, 0.233579490274, -0.00775639696254), (-0.00776439956516, -0.000885273943777, -0.999969464729)49.7029881644, -36.9752294146, 382.573114049
13given(-0.889550948631, -0.456266404475, 0.0228052173322), (-0.456303312904, 0.889815921479, 0.00386167252766), (-0.0220543969145, -0.0069709417599, -0.999732468987)439.714046393, 107.206287375, 386.786466224
14given(-0.907027751872, 0.421046322396, -0.00454441757435), (-0.421043242853, -0.907039044838, -0.00166095956815), (-0.0048213050938, 0.00040685988933, 0.999988294673)283.956204804, 444.31842389, 0.51949917651
15given(-0.886036305622, -0.463454893195, -0.0122158541472), (0.463397883611, -0.886120131962, 0.00731527141738), (-0.0142150126224, 0.000820795102961, 0.999898624717)451.25586108, 270.094801044, 1.7851004513
16given(-0.201043340751, -0.979571241158, -0.00466461538229), (0.979551509393, -0.201072516533, 0.00697735911338), (-0.00777274628027, -0.00316647945269, 0.999964778291)417.063444385, 40.3250587503, 1.7738041913
17given(0.630257485872, -0.776377515886, 0.00366801423618), (0.776362288818, 0.630268121047, 0.00486745245471), (-0.0060908130861, -0.000220040418892, 0.999981426617)217.449550823, -78.8249155639, 0.828507129154
18given(-0.23800414238, 0.971244454756, 0.00618363284), (-0.971245356656, -0.237955122358, -0.00773413975134), (-0.00604031323673, -0.00784658198169, 0.999950971682)48.8693767541, 422.845563336, 2.50211998877
19given(0.614726831882, 0.788720282066, -0.0055891700683), (-0.7887148912, 0.614748400367, 0.0036365705906), (0.00630417034083, 0.00217276414424, 0.999977768019)-76.2207283993, 222.790810658, -1.34364698024
20given(-0.897979245763, -0.440016825173, -0.00429741119508), (-0.440022273834, 0.897986783899, 0.000366704095328), (0.00369766248636, 0.0022202493126, -0.999990698849)446.337977911, 103.049128804, 379.795596208
21given(-0.203758153449, -0.979014933582, -0.00351777286465), (-0.978981490094, 0.203780946552, -0.00828057223064), (0.00882365895652, 0.00175660041363, -0.99995952788)417.245787787, 340.176329182, 379.244458735
22given(0.645944038428, -0.763324840433, 0.00956489395994), (-0.763291783786, -0.646010215183, -0.00751363323579), (0.011914362096, -0.00244741837681, -0.999926026324)211.136938762, 461.626479683, 379.66236782
23given(0.999881390483, 0.0147899619363, 0.00429674209051), (0.0147968853315, -0.999889265409, -0.00158401504184), (0.00427283877036, 0.0016474055626, -0.999989514397)-4.1767378379, 378.791841276, 379.922656483
24given(0.615234804462, 0.788306229642, -0.00770867607868), (0.788306667164, -0.615271378815, -0.00370525507669), (-0.00766380341914, -0.00379719886525, -0.99996342303)-75.620256939, 158.164865432, 382.718832234
25given(-0.905633567908, 0.424023685914, 0.00563510980952), (0.424008668322, 0.905650594063, -0.00369468007753), (-0.00667007241135, -0.000956690894711, -0.999977297181)281.040737634, -62.5621955235, 381.99605892
26given(-0.222061657265, 0.975032590973, 0.000258677123082), (0.975032547551, 0.222061737685, -0.000340401239334), (-0.000389344593809, 0.00017662855097, -0.999999908607)47.1373184611, -37.4944666247, 380.818108596

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Components

#1: Protein
60 kDa heat shock protein, mitochondrial / 60 kDa chaperonin / Chaperonin 60 / CPN60 / Heat shock protein 60 / HSP-60 / Hsp60 / Heat shock ...60 kDa chaperonin / Chaperonin 60 / CPN60 / Heat shock protein 60 / HSP-60 / Hsp60 / Heat shock protein family D member 1 / HuCHA60 / Mitochondrial matrix protein P1 / P60 lymphocyte protein


Mass: 61132.523 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P10809, chaperonin ATPase
#2: Protein
10 kDa heat shock protein, mitochondrial / Hsp10 / 10 kDa chaperonin / Chaperonin 10 / CPN10 / Early-pregnancy factor / EPF / Heat shock ...Hsp10 / 10 kDa chaperonin / Chaperonin 10 / CPN10 / Early-pregnancy factor / EPF / Heat shock protein family E member 1


Mass: 10946.674 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P61604
#3: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#4: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: CELL / 3D reconstruction method: subtomogram averaging

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Sample preparation

ComponentName: in situ human mtHsp60-Hsp10 football complex / Type: CELL / Entity ID: #1-#2 / Source: NATURAL
Source (natural)Organism: Homo sapiens (human)
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: OTHER / Nominal defocus max: 4800 nm / Nominal defocus min: 3000 nm
Image recordingElectron dose: 3.2 e/Å2 / Avg electron dose per subtomogram: 131 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

CTF correctionType: NONE
SymmetryPoint symmetry: D7 (2x7 fold dihedral)
3D reconstructionResolution: 7.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 6735 / Symmetry type: POINT
EM volume selectionNum. of tomograms: 169 / Num. of volumes extracted: 43800
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 61.24 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.003766696
ELECTRON MICROSCOPYf_angle_d0.870190020
ELECTRON MICROSCOPYf_chiral_restr0.054810850
ELECTRON MICROSCOPYf_plane_restr0.005311522
ELECTRON MICROSCOPYf_dihedral_angle_d4.90739408
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2TQELECTRON MICROSCOPYNCS constraints2.41817005239E-13
ens_1d_3TQELECTRON MICROSCOPYNCS constraints3.57647122727E-11
ens_1d_4TQELECTRON MICROSCOPYNCS constraints7.33651641082E-12
ens_1d_5TQELECTRON MICROSCOPYNCS constraints2.07692963174E-10
ens_1d_6TQELECTRON MICROSCOPYNCS constraints3.02588940917E-10
ens_1d_7TQELECTRON MICROSCOPYNCS constraints4.41007073642E-13
ens_1d_8TQELECTRON MICROSCOPYNCS constraints2.91106213108E-12
ens_1d_9TQELECTRON MICROSCOPYNCS constraints3.17064973662E-12
ens_1d_10TQELECTRON MICROSCOPYNCS constraints1.25019165638E-13
ens_1d_11TQELECTRON MICROSCOPYNCS constraints1.292329628E-13
ens_1d_12TQELECTRON MICROSCOPYNCS constraints1.56005575974E-12
ens_1d_13TQELECTRON MICROSCOPYNCS constraints3.06525212788E-11
ens_1d_14TQELECTRON MICROSCOPYNCS constraints3.69315426538E-12
ens_2d_2CFELECTRON MICROSCOPYNCS constraints5.7377765134E-11
ens_2d_3CFELECTRON MICROSCOPYNCS constraints2.88825651968E-10
ens_2d_4CFELECTRON MICROSCOPYNCS constraints2.16876712979E-11
ens_2d_5CFELECTRON MICROSCOPYNCS constraints4.82749963276E-13
ens_2d_6CFELECTRON MICROSCOPYNCS constraints4.68623488158E-13
ens_2d_7CFELECTRON MICROSCOPYNCS constraints1.94193457323E-12
ens_2d_8CFELECTRON MICROSCOPYNCS constraints4.38328455942E-13
ens_2d_9CFELECTRON MICROSCOPYNCS constraints4.35301740607E-13
ens_2d_10CFELECTRON MICROSCOPYNCS constraints3.17814389114E-13
ens_2d_11CFELECTRON MICROSCOPYNCS constraints3.04415501023E-11
ens_2d_12CFELECTRON MICROSCOPYNCS constraints5.85324999798E-12
ens_2d_13CFELECTRON MICROSCOPYNCS constraints3.62713345758E-13
ens_2d_14CFELECTRON MICROSCOPYNCS constraints1.67591694929E-13

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Yorodumi

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  • 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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