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- PDB-4u0d: Hexameric HIV-1 CA in complex with Nup153 peptide, P212121 crysta... -

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Basic information

Entry
Database: PDB / ID: 4u0d
TitleHexameric HIV-1 CA in complex with Nup153 peptide, P212121 crystal form
Components
  • Gag polyprotein
  • Nuclear pore complex protein Nup153
KeywordsVIRAL PROTEIN / Capsid
Function / homology
Function and homology information


negative regulation of RNA export from nucleus / nuclear pore complex assembly / Nuclear Pore Complex (NPC) Disassembly / nuclear inclusion body / nuclear pore nuclear basket / Transport of Ribonucleoproteins into the Host Nucleus / Regulation of Glucokinase by Glucokinase Regulatory Protein / Defective TPR may confer susceptibility towards thyroid papillary carcinoma (TPC) / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA ...negative regulation of RNA export from nucleus / nuclear pore complex assembly / Nuclear Pore Complex (NPC) Disassembly / nuclear inclusion body / nuclear pore nuclear basket / Transport of Ribonucleoproteins into the Host Nucleus / Regulation of Glucokinase by Glucokinase Regulatory Protein / Defective TPR may confer susceptibility towards thyroid papillary carcinoma (TPC) / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / NS1 Mediated Effects on Host Pathways / SUMOylation of SUMOylation proteins / Transport of Mature mRNA Derived from an Intronless Transcript / Rev-mediated nuclear export of HIV RNA / structural constituent of nuclear pore / SUMOylation of RNA binding proteins / Nuclear import of Rev protein / Transport of Mature mRNA derived from an Intron-Containing Transcript / NEP/NS2 Interacts with the Cellular Export Machinery / tRNA processing in the nucleus / RNA export from nucleus / nucleocytoplasmic transport / Viral Messenger RNA Synthesis / nuclear localization sequence binding / SUMOylation of ubiquitinylation proteins / viral budding via host ESCRT complex / Vpr-mediated nuclear import of PICs / SUMOylation of DNA replication proteins / Regulation of HSF1-mediated heat shock response / mRNA transport / SUMOylation of DNA damage response and repair proteins / nuclear pore / protein-membrane adaptor activity / SUMOylation of chromatin organization proteins / nuclear periphery / HCMV Late Events / molecular condensate scaffold activity / Transcriptional regulation by small RNAs / ISG15 antiviral mechanism / host multivesicular body / HCMV Early Events / viral penetration into host nucleus / protein import into nucleus / host cell / nuclear envelope / snRNP Assembly / viral nucleocapsid / nuclear membrane / amyloid fibril formation / symbiont entry into host cell / host cell nucleus / nucleolus / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / structural molecule activity / virion membrane / DNA binding / RNA binding / zinc ion binding / nucleoplasm / identical protein binding / membrane / metal ion binding / cytosol
Similarity search - Function
Nucleoporin Nup153, N-terminal / Retro-transposon transporting motif / Nucleoporin Nup153-like / Retro-transposon transporting motif / Nuclear pore complex protein / Retrovirus capsid C-terminal domain / Human Immunodeficiency Virus Type 1 Capsid Protein / Human Immunodeficiency Virus Type 1 Capsid Protein / Zinc finger domain / Gag protein p6 ...Nucleoporin Nup153, N-terminal / Retro-transposon transporting motif / Nucleoporin Nup153-like / Retro-transposon transporting motif / Nuclear pore complex protein / Retrovirus capsid C-terminal domain / Human Immunodeficiency Virus Type 1 Capsid Protein / Human Immunodeficiency Virus Type 1 Capsid Protein / Zinc finger domain / Gag protein p6 / Gag protein p6 / Zn-finger in Ran binding protein and others / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / Zinc finger RanBP2 type profile. / Zinc finger RanBP2-type signature. / Zinc finger, RanBP2-type superfamily / Zinc finger, RanBP2-type / gag protein p24 N-terminal domain / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retrovirus capsid, C-terminal / Retroviral matrix protein / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Gag polyprotein / Nuclear pore complex protein Nup153
Similarity search - Component
Biological speciesHuman immunodeficiency virus type 1 group M subtype B
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3 Å
AuthorsPrice, A.J. / Jacques, D.A. / James, L.C.
CitationJournal: Plos Pathog. / Year: 2014
Title: Host Cofactors and Pharmacologic Ligands Share an Essential Interface in HIV-1 Capsid That Is Lost upon Disassembly.
Authors: Price, A.J. / Jacques, D.A. / McEwan, W.A. / Fletcher, A.J. / Essig, S. / Chin, J.W. / Halambage, U.D. / Aiken, C. / James, L.C.
History
DepositionJul 11, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Nov 12, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Gag polyprotein
B: Gag polyprotein
C: Gag polyprotein
D: Gag polyprotein
E: Gag polyprotein
F: Gag polyprotein
G: Gag polyprotein
H: Gag polyprotein
I: Gag polyprotein
J: Gag polyprotein
K: Gag polyprotein
L: Gag polyprotein
M: Nuclear pore complex protein Nup153
N: Nuclear pore complex protein Nup153
O: Nuclear pore complex protein Nup153
P: Nuclear pore complex protein Nup153
Q: Nuclear pore complex protein Nup153
R: Nuclear pore complex protein Nup153
hetero molecules


Theoretical massNumber of molelcules
Total (without water)315,69719
Polymers315,66218
Non-polymers351
Water00
1
A: Gag polyprotein
B: Gag polyprotein
C: Gag polyprotein
D: Gag polyprotein
E: Gag polyprotein
F: Gag polyprotein
M: Nuclear pore complex protein Nup153
O: Nuclear pore complex protein Nup153
P: Nuclear pore complex protein Nup153
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,86610
Polymers157,8319
Non-polymers351
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17760 Å2
ΔGint-141 kcal/mol
Surface area60780 Å2
MethodPISA
2
G: Gag polyprotein
H: Gag polyprotein
I: Gag polyprotein
J: Gag polyprotein
K: Gag polyprotein
L: Gag polyprotein
N: Nuclear pore complex protein Nup153
Q: Nuclear pore complex protein Nup153
R: Nuclear pore complex protein Nup153


Theoretical massNumber of molelcules
Total (without water)157,8319
Polymers157,8319
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17180 Å2
ΔGint-134 kcal/mol
Surface area59260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.380, 138.060, 211.850
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H
91I
101J
111K
121L
12A
22B
32C
42D
52E
62F
72G
82H
92I
102J
112K
122L
13A
23B
33C
43D
53E
63F
73G
83H
93I
103J
113K
123L

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A1 - 87
2114B1 - 87
3114C1 - 87
4114D1 - 87
5114E1 - 87
6114F1 - 87
7114G1 - 87
8114H1 - 87
9114I1 - 87
10114J1 - 87
11114K1 - 87
12114L1 - 87
1126A146 - 999
2126B146 - 999
3126C146 - 999
4126D146 - 999
5126E146 - 999
6126F146 - 999
7126G146 - 999
8126H146 - 999
9126I146 - 999
10126J146 - 999
11126K146 - 999
12126L146 - 999
1134A96 - 145
2134B96 - 145
3134C96 - 145
4134D96 - 145
5134E96 - 145
6134F96 - 145
7134G96 - 145
8134H96 - 145
9134I96 - 145
10134J96 - 145
11134K96 - 145
12134L96 - 145

NCS ensembles :
ID
1
2
3
Detailsbiological unit is the same as asym.

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Components

#1: Protein
Gag polyprotein / Pr55Gag


Mass: 25461.271 Da / Num. of mol.: 12 / Mutation: yes
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 group M subtype B
Strain: isolate NY5 / Gene: gag / Plasmid: pET11a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P12493
#2: Protein/peptide
Nuclear pore complex protein Nup153 / 153 kDa nucleoporin / Nucleoporin Nup153


Mass: 1687.721 Da / Num. of mol.: 6 / Fragment: UNP residues 1407-1423 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P49790
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl

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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: 3.14 Å3/Da / Density % sol: 60.78 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 10% w/v PEG 8K, 0.1M imidazole

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jan 20, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 3→46.07 Å / Num. obs: 77432 / Redundancy: 3.2 % / Rmerge(I) obs: 0.101 / Net I/σ(I): 8.6
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
3-3.063.10.6641.71349943900.5770.43697.3
15.3-46.073.30.02133.821546510.9990.01495.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3 Å46.07 Å
Translation3 Å46.07 Å

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Processing

Software
NameVersionClassification
Aimless0.2.7data scaling
PDB_EXTRACT3.14data extraction
PHASERphasing
iMOSFLMdata reduction
REFMAC5.8.0073refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3H47
Resolution: 3→115.67 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.901 / WRfactor Rfree: 0.2402 / WRfactor Rwork: 0.2209 / FOM work R set: 0.7754 / SU B: 46.735 / SU ML: 0.376 / SU R Cruickshank DPI: 0.3986 / SU Rfree: 0.4221 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.422 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.267 3884 5 %RANDOM
Rwork0.2457 73490 --
obs0.2468 77374 96.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 209.14 Å2 / Biso mean: 77.183 Å2 / Biso min: 33.36 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20 Å2
2--1.14 Å2-0 Å2
3----1.12 Å2
Refinement stepCycle: final / Resolution: 3→115.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19254 0 1 0 19255
Biso mean--58.41 --
Num. residues----2512
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.01919708
X-RAY DIFFRACTIONr_bond_other_d0.0010.0218755
X-RAY DIFFRACTIONr_angle_refined_deg0.6511.95926808
X-RAY DIFFRACTIONr_angle_other_deg0.656343214
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5265.0162480
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.51124.901812
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.163153266
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.94915103
X-RAY DIFFRACTIONr_chiral_restr0.0360.23059
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02122048
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024179
X-RAY DIFFRACTIONr_mcbond_it1.2866.1210012
X-RAY DIFFRACTIONr_mcbond_other1.2856.1210011
X-RAY DIFFRACTIONr_mcangle_it2.26310.30612440
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A1180MEDIUM POSITIONAL0.120.5
12B1180MEDIUM POSITIONAL0.10.5
13C1180MEDIUM POSITIONAL0.070.5
14D1180MEDIUM POSITIONAL0.080.5
15E1180MEDIUM POSITIONAL0.240.5
16F1180MEDIUM POSITIONAL0.080.5
17G1180MEDIUM POSITIONAL0.140.5
18H1180MEDIUM POSITIONAL0.120.5
19I1180MEDIUM POSITIONAL0.070.5
1101180MEDIUM POSITIONAL0.080.5
111A1180MEDIUM POSITIONAL0.070.5
112B1180MEDIUM POSITIONAL0.070.5
11A1180MEDIUM THERMAL7.422
12B1180MEDIUM THERMAL6.782
13C1180MEDIUM THERMAL6.022
14D1180MEDIUM THERMAL5.422
15E1180MEDIUM THERMAL6.472
16F1180MEDIUM THERMAL5.092
17G1180MEDIUM THERMAL5.242
18H1180MEDIUM THERMAL8.12
19I1180MEDIUM THERMAL6.982
1101180MEDIUM THERMAL5.582
111A1180MEDIUM THERMAL14.52
112B1180MEDIUM THERMAL11.42
21A871LOOSE POSITIONAL0.315
22B871LOOSE POSITIONAL0.355
23C871LOOSE POSITIONAL0.325
24D871LOOSE POSITIONAL0.335
25E871LOOSE POSITIONAL0.545
26F871LOOSE POSITIONAL0.575
27G871LOOSE POSITIONAL0.655
28H871LOOSE POSITIONAL0.355
29I871LOOSE POSITIONAL0.225
210871LOOSE POSITIONAL0.225
211A871LOOSE POSITIONAL0.285
212B871LOOSE POSITIONAL0.435
21A871LOOSE THERMAL6.5610
22B871LOOSE THERMAL10.8610
23C871LOOSE THERMAL3.0110
24D871LOOSE THERMAL10.2810
25E871LOOSE THERMAL11.4710
26F871LOOSE THERMAL10.5410
27G871LOOSE THERMAL14.4910
28H871LOOSE THERMAL5.8110
29I871LOOSE THERMAL6.5810
210871LOOSE THERMAL14.9710
211A871LOOSE THERMAL22.2510
212B871LOOSE THERMAL8.8110
31A681MEDIUM POSITIONAL0.090.5
32B681MEDIUM POSITIONAL0.060.5
33C681MEDIUM POSITIONAL0.080.5
34D681MEDIUM POSITIONAL0.080.5
35E681MEDIUM POSITIONAL0.10.5
36F681MEDIUM POSITIONAL0.10.5
37G681MEDIUM POSITIONAL0.10.5
38H681MEDIUM POSITIONAL0.090.5
39I681MEDIUM POSITIONAL0.070.5
310681MEDIUM POSITIONAL0.060.5
311A681MEDIUM POSITIONAL0.080.5
312B681MEDIUM POSITIONAL0.090.5
31A681MEDIUM THERMAL10.442
32B681MEDIUM THERMAL5.422
33C681MEDIUM THERMAL4.832
34D681MEDIUM THERMAL3.472
35E681MEDIUM THERMAL8.362
36F681MEDIUM THERMAL4.462
37G681MEDIUM THERMAL5.62
38H681MEDIUM THERMAL11.752
39I681MEDIUM THERMAL4.62
310681MEDIUM THERMAL6.022
311A681MEDIUM THERMAL14.322
312B681MEDIUM THERMAL13.652
LS refinement shellResolution: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.39 252 -
Rwork0.365 5439 -
all-5691 -
obs--96.93 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.02130.0293-0.3522.93730.53153.5548-0.00330.03240.2198-0.02930.0135-0.4005-0.47450.249-0.01030.1635-0.051-0.10890.13820.05530.2033-35.5389-30.83529.5396
22.5381-0.456-2.07832.13140.94843.6231-0.1492-0.4290.24770.18140.1522-0.0874-0.07740.3179-0.00310.21280.0862-0.1720.1042-0.08140.1518-40.4188-29.479837.4783
32.47690.87690.11931.91040.61041.9651-0.1349-0.5240.29290.21620.06830.1049-0.0932-0.3960.06660.16330.18520.02010.3321-0.02090.0973-56.7586-47.148448.9212
42.2574-0.02180.82460.5525-0.31663.5812-0.09680.0255-0.2473-0.02270.16360.04590.3288-1.0155-0.06680.0529-0.09370.02240.37920.01060.0526-71.0031-64.746933.7449
50.9775-0.47840.57730.8523-1.05016.32620.06120.0273-0.0983-0.04010.08980.09390.8407-0.5008-0.15090.1522-0.1132-0.01220.18240.03370.0494-67.8825-64.51456.1992
61.09930.90550.58614.0687-0.21681.8734-0.06870.1269-0.0693-0.2503-0.0176-0.0529-0.07940.03190.08630.0289-0.0008-0.00780.1710.02930.029-50.2339-48.0406-5.7548
74.7530.22210.54260.8727-0.46441.70940.0767-0.18930.10030.0048-0.02870.02020.0284-0.0052-0.0480.04940.03410.01370.15690.09070.0683-13.2656-85.412258.7519
83.9562-0.3780.19331.40660.40323.27420.0110.26530.7743-0.0792-0.0989-0.3637-0.29630.52260.08790.09070.00270.04820.30140.26330.37572.8652-70.194544.1887
91.81090.7344-0.46462.80230.82344.2020.18250.29620.0515-0.43-0.3234-0.4698-0.16420.39810.14090.21490.29540.23790.52120.3750.30084.5844-74.54716.9582
101.32590.7539-0.09473.1274-0.21162.7870.10670.3446-0.1873-0.7472-0.3517-0.3141.0490.16230.24490.70720.36530.19180.36360.09110.107-11.5281-90.79854.7147
110.88360.2993-0.18213.3134-1.71294.08440.29210.11-0.0314-0.50250.01750.22511.4935-0.4485-0.30960.8644-0.0568-0.10940.20440.06180.0429-28.8262-105.509218.7843
121.0899-0.6081.18741.3208-0.47987.9340.1241-0.04420.0367-0.1655-0.0068-0.04720.7008-1.2311-0.11730.1943-0.1631-0.06770.27550.08090.0544-28.823-103.458646.9323
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 219
2X-RAY DIFFRACTION2B1 - 219
3X-RAY DIFFRACTION3C1 - 219
4X-RAY DIFFRACTION4D1 - 219
5X-RAY DIFFRACTION5E1 - 219
6X-RAY DIFFRACTION6F1 - 219
7X-RAY DIFFRACTION7G1 - 219
8X-RAY DIFFRACTION8H1 - 999
9X-RAY DIFFRACTION9I1 - 219
10X-RAY DIFFRACTION10J1 - 219
11X-RAY DIFFRACTION11K1 - 219
12X-RAY DIFFRACTION12L1 - 219

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