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- PDB-6cgv: Revised crystal structure of human adenovirus -

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Basic information

Entry
Database: PDB / ID: 6cgv
TitleRevised crystal structure of human adenovirus
Components
  • (Pre-hexon-linking protein ...) x 2
  • Hexon protein
  • Hexon-interlacing protein
  • Penton protein
  • Pre-protein VI
KeywordsVIRUS / Human adenovirus Crystal structure Ad5F35 Ad35F
Function / homology
Function and homology information


hexon binding / protein transport along microtubule / viral capsid, decoration / T=25 icosahedral viral capsid / lysis of host organelle involved in viral entry into host cell / viral procapsid / microtubule-dependent intracellular transport of viral material towards nucleus / viral release from host cell / viral life cycle / viral capsid ...hexon binding / protein transport along microtubule / viral capsid, decoration / T=25 icosahedral viral capsid / lysis of host organelle involved in viral entry into host cell / viral procapsid / microtubule-dependent intracellular transport of viral material towards nucleus / viral release from host cell / viral life cycle / viral capsid / clathrin-dependent endocytosis of virus by host cell / host cell cytoplasm / symbiont entry into host cell / host cell nucleus / virion attachment to host cell / structural molecule activity
Similarity search - Function
Pre-hexon-linking protein IIIa / Pre-hexon-linking protein IIIa / Hexon-associated protein IX / Pre-hexon-linking protein IIIa, N-terminal / Hexon-associated protein (IIIa) / Adenovirus hexon-associated protein (IX) / Pre-hexon-linking protein VIII / Adenovirus hexon associated protein, protein VIII / Adenovirus Pll, hexon, subdomain 2 / Minor capsid protein VI ...Pre-hexon-linking protein IIIa / Pre-hexon-linking protein IIIa / Hexon-associated protein IX / Pre-hexon-linking protein IIIa, N-terminal / Hexon-associated protein (IIIa) / Adenovirus hexon-associated protein (IX) / Pre-hexon-linking protein VIII / Adenovirus hexon associated protein, protein VIII / Adenovirus Pll, hexon, subdomain 2 / Minor capsid protein VI / Minor capsid protein VI / Adenovirus hexon protein / Adenovirus Pll, hexon, N-terminal / Adenovirus Pll, hexon, C-terminal / Hexon, adenovirus major coat protein, N-terminal domain / Hexon, adenovirus major coat protein, C-terminal domain / Adenovirus penton base protein / Adenovirus penton base protein / Group II dsDNA virus coat/capsid protein / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Hexon-interlacing protein / Hexon protein / Pre-hexon-linking protein IIIa / Penton protein / Pre-hexon-linking protein VIII / Pre-protein VI
Similarity search - Component
Biological speciesHuman adenovirus C serotype 5
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.8 Å
AuthorsNatchiar, S.K. / Venkataraman, S. / Nemerow, G.R. / Reddy, V.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI070771 United States
Citation
Journal: J. Mol. Biol. / Year: 2018
Title: Revised Crystal Structure of Human Adenovirus Reveals the Limits on Protein IX Quasi-Equivalence and on Analyzing Large Macromolecular Complexes.
Authors: Kundhavai Natchiar, S. / Venkataraman, S. / Mullen, T.M. / Nemerow, G.R. / Reddy, V.S.
#1: Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2014
Title: Structures and organization of adenovirus cement proteins provide insights into the role of capsid maturation in virus entry and infection.
Authors: Reddy, V.S. / Nemerow, G.R.
History
DepositionFeb 21, 2018Deposition site: RCSB / Processing site: RCSB
SupersessionApr 25, 2018ID: 4CWU
Revision 1.0Apr 25, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 5, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 24, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hexon protein
B: Hexon protein
C: Hexon protein
D: Hexon protein
E: Hexon protein
F: Hexon protein
G: Hexon protein
H: Hexon protein
I: Hexon protein
J: Hexon protein
K: Hexon protein
L: Hexon protein
N: Penton protein
M: Pre-hexon-linking protein IIIa
P: Hexon-interlacing protein
Q: Hexon-interlacing protein
R: Hexon-interlacing protein
S: Hexon-interlacing protein
U: Pre-hexon-linking protein VIII
V: Pre-hexon-linking protein VIII
W: Pre-protein VI


Theoretical massNumber of molelcules
Total (without water)1,532,27421
Polymers1,532,27421
Non-polymers00
Water0
1
A: Hexon protein
B: Hexon protein
C: Hexon protein
D: Hexon protein
E: Hexon protein
F: Hexon protein
G: Hexon protein
H: Hexon protein
I: Hexon protein
J: Hexon protein
K: Hexon protein
L: Hexon protein
N: Penton protein
M: Pre-hexon-linking protein IIIa
P: Hexon-interlacing protein
Q: Hexon-interlacing protein
R: Hexon-interlacing protein
S: Hexon-interlacing protein
U: Pre-hexon-linking protein VIII
V: Pre-hexon-linking protein VIII
W: Pre-protein VI
x 60


Theoretical massNumber of molelcules
Total (without water)91,936,4371260
Polymers91,936,4371260
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation60
2


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
point symmetry operation1
3
A: Hexon protein
B: Hexon protein
C: Hexon protein
D: Hexon protein
E: Hexon protein
F: Hexon protein
G: Hexon protein
H: Hexon protein
I: Hexon protein
J: Hexon protein
K: Hexon protein
L: Hexon protein
N: Penton protein
M: Pre-hexon-linking protein IIIa
P: Hexon-interlacing protein
Q: Hexon-interlacing protein
R: Hexon-interlacing protein
S: Hexon-interlacing protein
U: Pre-hexon-linking protein VIII
V: Pre-hexon-linking protein VIII
W: Pre-protein VI
x 5


  • icosahedral pentamer
  • 7.66 MDa, 105 polymers
Theoretical massNumber of molelcules
Total (without water)7,661,370105
Polymers7,661,370105
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation5
4
A: Hexon protein
B: Hexon protein
C: Hexon protein
D: Hexon protein
E: Hexon protein
F: Hexon protein
G: Hexon protein
H: Hexon protein
I: Hexon protein
J: Hexon protein
K: Hexon protein
L: Hexon protein
N: Penton protein
M: Pre-hexon-linking protein IIIa
P: Hexon-interlacing protein
Q: Hexon-interlacing protein
R: Hexon-interlacing protein
S: Hexon-interlacing protein
U: Pre-hexon-linking protein VIII
V: Pre-hexon-linking protein VIII
W: Pre-protein VI
x 6


  • icosahedral 23 hexamer
  • 9.19 MDa, 126 polymers
Theoretical massNumber of molelcules
Total (without water)9,193,644126
Polymers9,193,644126
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation6
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
6
A: Hexon protein
B: Hexon protein
C: Hexon protein
D: Hexon protein
E: Hexon protein
F: Hexon protein
G: Hexon protein
H: Hexon protein
I: Hexon protein
J: Hexon protein
K: Hexon protein
L: Hexon protein
N: Penton protein
M: Pre-hexon-linking protein IIIa
P: Hexon-interlacing protein
Q: Hexon-interlacing protein
R: Hexon-interlacing protein
S: Hexon-interlacing protein
U: Pre-hexon-linking protein VIII
V: Pre-hexon-linking protein VIII
W: Pre-protein VI
x 60


  • crystal asymmetric unit, crystal frame
  • 91.9 MDa, 1260 polymers
Theoretical massNumber of molelcules
Total (without water)91,936,4371260
Polymers91,936,4371260
Non-polymers00
Water0
TypeNameSymmetry operationNumber
transform to crystal frame1
point symmetry operation60
Unit cell
Length a, b, c (Å)854.245, 855.315, 865.907
Angle α, β, γ (deg.)60.38, 60.43, 61.98
Int Tables number1
Space group name H-MP1
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrix
1given(1), (1), (1)
2generate(0.32439977, 0.23824617, 0.91542535), (-0.42887783, 0.89961938, -0.08215087), (-0.8431065, -0.36595592, 0.39401483)
3generate(-0.76874435, -0.04338745, 0.63808281), (-0.45569275, 0.73720013, -0.49887882), (-0.44874964, -0.67427999, -0.58648977)
4generate(-0.76874434, -0.45569277, -0.44874965), (-0.04338745, 0.73720013, -0.67427998), (0.6380828, -0.49887883, -0.58648978)
5generate(0.32439978, -0.42887785, -0.84310651), (0.23824616, 0.89961938, -0.36595592), (0.91542533, -0.08215087, 0.39401482)
6generate(-0.69122041, 0.67558093, -0.25652438), (0.67558093, 0.47810802, -0.56125139), (-0.25652437, -0.56125139, -0.78688762)
7generate(-0.29769606, 0.5369617, -0.78933465), (0.48730306, 0.79646308, 0.35802554), (0.8209219, -0.2780624, -0.49876702)
8generate(0.33862967, 0.7009979, -0.62763995), (-0.48535802, 0.70159014, 0.52172681), (0.80607539, 0.12795791, 0.57781418)
9generate(0.33837625, 0.94099707, 0.00510314), (-0.89821776, 0.32460039, -0.29637717), (-0.28054653, 0.09570327, 0.95505735)
10generate(-0.2981061, 0.92528852, 0.23446518), (-0.18071803, 0.18648084, -0.96569451), (-0.9372693, -0.3302515, 0.11162525)
11generate(0.69121986, -0.67595115, 0.25554872), (-0.67595114, -0.72983409, -0.10213838), (0.25554873, -0.10213838, -0.96138577)
12generate(0.29867724, -0.53693784, 0.78898014), (0.1798448, -0.78023752, -0.59907033), (0.93725543, 0.32082265, -0.13647371)
13generate(-0.33802272, -0.70061293, 0.62839651), (0.89804828, -0.43983613, -0.00731092), (0.2815136, 0.56185915, 0.77785885)
14generate(-0.33898232, -0.94078301, -0.00428106), (0.48612651, -0.17905307, 0.85534847), (-0.80546384, 0.28786687, 0.51803539)
15generate(0.29712458, -0.92554119, -0.23471366), (-0.48665863, -0.35828167, 0.79674188), (-0.82151101, -0.12250618, -0.5568769)
16generate(-0.99999946, 0.00037022, 0.00097565), (0.00037021, -0.74827393, 0.66338977), (0.00097564, 0.66338977, 0.74827339)
17generate(-0.32538095, -0.23827003, -0.91507084), (-0.23827002, -0.91584494, 0.32319566), (-0.91507083, 0.32319567, 0.24122589)
18generate(0.7681374, 0.04300249, -0.63883937), (0.04300249, -0.99895415, -0.01553707), (-0.63883935, -0.01553707, -0.76918325)
19generate(0.76935041, 0.45547871, 0.44792756), (0.4554787, -0.88274745, 0.11530868), (0.44792757, 0.11530869, -0.88660296)
20generate(-0.32341827, 0.42913052, 0.84335499), (0.4291305, -0.72781856, 0.53490854), (0.84335498, 0.53490855, 0.05123682)
21generate(-0.36104716, 0.47020323, 0.80532844), (-0.93012904, -0.11941809, -0.34727406), (-0.06711861, -0.87444167, 0.48046525)
22generate(-0.997761, 0.04227114, -0.05182797), (0.04227114, -0.20194351, -0.97848453), (-0.05182799, -0.97848453, 0.19970451)
23generate(-0.29810609, -0.18071805, -0.93726931), (0.92528851, 0.18648085, -0.33025151), (0.23446517, -0.96569451, 0.11162524)
24generate(0.77101826, 0.10939916, -0.62734574), (0.49862307, 0.50906572, 0.701589), (0.39611345, -0.85374699, 0.33795001)
25generate(0.73211854, 0.51169064, 0.4496389), (-0.64808803, 0.32000978, 0.69106848), (0.20972443, -0.79734963, 0.56590567)
26generate(0.36063713, -0.47110034, -0.8049878), (0.65133185, -0.49056414, 0.57889), (-0.66761341, -0.73308342, 0.12992701)
27generate(0.99772554, -0.04330054, 0.05166054), (-0.06638193, -0.49799191, 0.8646372), (-0.01171271, -0.86609995, -0.49973363)
28generate(0.29867724, 0.1798448, 0.93725544), (-0.53693784, -0.78023752, 0.32082265), (0.78898014, -0.59907033, -0.13647371)
29generate(-0.77044677, -0.1100436, 0.62793486), (-0.1100436, -0.94724712, -0.30102043), (0.62793484, -0.30102042, 0.7176939)
30generate(-0.73215346, -0.51234982, -0.44883068), (0.62434746, -0.76821913, -0.14152604), (-0.27228948, -0.38384507, 0.8823386)
31generate(-0.36159672, -0.18137505, -0.91452223), (-0.65094832, 0.75134719, 0.10836823), (0.66746841, 0.6344923, -0.38975048)
32generate(0.73152549, 0.08535728, -0.67645001), (-0.6247696, 0.48118256, -0.61491973), (0.27300808, 0.87245486, 0.40532594)
33generate(0.77101826, 0.49862309, 0.39611346), (0.10939917, 0.50906571, -0.85374699), (-0.62734572, 0.701589, 0.33795002)
34generate(-0.29769607, 0.48730307, 0.82092191), (0.5369617, 0.79646308, -0.2780624), (-0.78933464, 0.35802554, -0.498767)
35generate(-0.99769062, 0.06704111, 0.01090451), (0.06704111, 0.94620127, 0.3165575), (0.01090451, 0.3165575, -0.94851064)
36generate(0.36200675, 0.18227216, 0.91418159), (0.92974551, -0.14136497, -0.33998416), (0.0672636, 0.97303279, -0.22064178)
37generate(-0.73149003, -0.08432788, 0.67661745), (0.64888039, 0.21875285, 0.72876705), (-0.20946738, 0.97212962, -0.10529682)
38generate(-0.77158941, -0.49774984, -0.39609959), (-0.49774984, 0.08469096, 0.86317585), (-0.39609958, 0.86317584, -0.31310155)
39generate(0.29712459, -0.48665864, -0.82151103), (-0.92554117, -0.35828167, -0.12250617), (-0.23471365, 0.79674187, -0.5568769)
40generate(0.99772554, -0.06638192, -0.01171273), (-0.04330053, -0.49799192, -0.86609994), (0.05166055, 0.8646372, -0.49973362)
41generate(-0.36104715, -0.93012906, -0.0671186), (0.47020323, -0.11941809, -0.87444168), (0.80532841, -0.34727407, 0.48046524)
42generate(0.33837625, -0.89821778, -0.28054653), (0.94099705, 0.3246004, 0.09570326), (0.00510313, -0.29637717, 0.95505734)
43generate(0.73152548, -0.62476961, 0.27300807), (0.08535727, 0.48118257, 0.87245485), (-0.67645, -0.61491973, 0.40532594)
44generate(0.27508165, -0.48768063, 0.82855156), (-0.91425102, 0.13393719, 0.3823688), (-0.29744772, -0.86268676, -0.40901885)
45generate(-0.40016537, -0.67640315, 0.61834171), (-0.67640313, -0.23725443, -0.69727263), (0.61834171, -0.69727264, -0.3625802)
46generate(-0.36159673, -0.65094833, 0.66746842), (-0.18137505, 0.7513472, 0.6344923), (-0.91452222, 0.10836821, -0.38975047)
47generate(-0.40087155, -0.91601879, -0.01454638), (-0.91601877, 0.40051838, 0.02224024), (-0.01454637, 0.02224022, -0.99964683)
48generate(0.27508166, -0.91425103, -0.29744773), (-0.48768062, 0.13393719, -0.86268675), (0.82855156, 0.38236879, -0.40901885)
49generate(0.73211854, -0.64808804, 0.20972443), (0.51169063, 0.32000977, -0.79734964), (0.44963889, 0.69106848, 0.56590567)
50generate(0.33862966, -0.48535802, 0.8060754), (0.70099789, 0.70159014, 0.12795791), (-0.62763995, 0.52172681, 0.57781419)
51generate(0.36200676, 0.92974552, 0.0672636), (0.18227214, -0.14136496, 0.97303279), (0.91418158, -0.33998415, -0.22064179)
52generate(-0.33802272, 0.8980483, 0.28151361), (-0.70061293, -0.43983613, 0.56185915), (0.6283965, -0.00731091, 0.77785884)
53generate(-0.73215346, 0.62434747, -0.27228947), (-0.51234981, -0.76821913, -0.38384507), (-0.44883068, -0.14152603, 0.8823386)
54generate(-0.27571018, 0.48688827, -0.82880861), (0.48688827, -0.67269982, -0.55714878), (-0.8288086, -0.55714878, -0.05159)
55generate(0.40051802, 0.67563465, -0.61895327), (0.91618825, -0.28528264, 0.28144785), (0.0135793, -0.67980265, -0.73326937)
56generate(0.36063713, 0.65133186, -0.66761342), (-0.47110033, -0.49056415, -0.73308342), (-0.80498778, 0.57889001, 0.12992702)
57generate(0.40051802, 0.91618827, 0.0135793), (0.67563464, -0.28528264, -0.67980265), (-0.61895326, 0.28144786, -0.73326936)
58generate(-0.27445368, 0.91467318, 0.29672913), (0.91467316, 0.15309937, 0.37407697), (0.29672912, 0.37407697, -0.87864569)
59generate(-0.73149002, 0.6488804, -0.20946737), (-0.08432788, 0.21875285, 0.97212962), (0.67661743, 0.72876706, -0.10529683)
60generate(-0.33898231, 0.48612652, -0.80546384), (-0.940783, -0.17905308, 0.28786687), (-0.00428106, 0.85534848, 0.51803539)

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Components

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Protein , 3 types, 17 molecules ABCDEFGHIJKLNPQRS

#1: Protein
Hexon protein / / CP-H / Protein II


Mass: 107804.242 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human adenovirus C serotype 5 / Gene: L3 / Production host: Homo sapiens (human) / References: UniProt: P04133
#2: Protein Penton protein / / CP-P / Penton base protein / Protein III


Mass: 63356.602 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human adenovirus C serotype 5 / Gene: L2 / Production host: Homo sapiens (human) / References: UniProt: P12538
#4: Protein
Hexon-interlacing protein / Protein IX


Mass: 14468.134 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human adenovirus C serotype 5 / Gene: IX / Production host: Homo sapiens (human) / References: UniProt: P03281

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Pre-hexon-linking protein ... , 2 types, 3 molecules MUV

#3: Protein Pre-hexon-linking protein IIIa / Capsid vertex-specific component IIIa / CVSC / Protein IIIa / pIIIa


Mass: 65322.805 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human adenovirus C serotype 5 / Gene: L1 / Production host: Homo sapiens (human) / References: UniProt: P12537
#5: Protein Pre-hexon-linking protein VIII / Pre-protein VIII / pVIII


Mass: 24710.590 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human adenovirus C serotype 5 / Gene: L4 / Production host: Homo sapiens (human) / References: UniProt: P24936

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Protein/peptide , 1 types, 1 molecules W

#6: Protein/peptide Pre-protein VI / pVI


Mass: 2649.918 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human adenovirus C serotype 5 / Gene: L3 / Production host: Homo sapiens (human) / References: UniProt: P24937

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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: 3.04 Å3/Da / Density % sol: 60 % / Description: Trapazoidal
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 100MM HEPES PH 7.0, 200MM CALCIUM ACETATE, 14% PEG550 MME, 15% GLYCEROL.
PH range: 6.5-7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.85506 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Nov 1, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.85506 Å / Relative weight: 1
ReflectionResolution: 3.8→129 Å / Num. obs: 15015304 / % possible obs: 53.2 % / Observed criterion σ(F): 1.1 / Redundancy: 1.6 % / Biso Wilson estimate: 20.04 Å2 / Rsym value: 0.363 / Net I/σ(I): 2.8
Reflection shellResolution: 3.8→3.9 Å

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Processing

Software
NameVersionClassification
REFMAC5.8refinement
HKL-2000data reduction
SCALAdata scaling
PHASERphasing
RefinementResolution: 3.8→129 Å
RfactorNum. reflection
Rfree0.427 -
Rwork0.422 -
obs-15015304

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