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- PDB-4x7f: Crystal structure of norovirus GII.10 P domain in complex with Nano-25 -

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Basic information

Entry
Database: PDB / ID: 4x7f
TitleCrystal structure of norovirus GII.10 P domain in complex with Nano-25
Components
  • Capsid protein
  • Nano-25 Nanobody
KeywordsVIRAL PROTEIN / Nanobody / VHH domain / Norovirus / Protruding domain
Function / homology
Function and homology information


Positive stranded ssRNA viruses / Nucleoplasmin-like/VP (viral coat and capsid proteins) / Positive stranded ssRNA viruses / Calicivirus coat protein C-terminal / Calicivirus coat protein C-terminal / Calicivirus coat protein / Calicivirus coat protein / Elongation Factor Tu (Ef-tu); domain 3 / Picornavirus/Calicivirus coat protein / Viral coat protein subunit ...Positive stranded ssRNA viruses / Nucleoplasmin-like/VP (viral coat and capsid proteins) / Positive stranded ssRNA viruses / Calicivirus coat protein C-terminal / Calicivirus coat protein C-terminal / Calicivirus coat protein / Calicivirus coat protein / Elongation Factor Tu (Ef-tu); domain 3 / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / Immunoglobulins / Immunoglobulin-like / Beta Barrel / Sandwich / Mainly Beta
Similarity search - Domain/homology
IMIDAZOLE / PHOSPHATE ION / Capsid protein
Similarity search - Component
Biological speciesNorwalk virus
Vicugna pacos (alpaca)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsKoromyslova, A.D. / Hansman, G.S.
CitationJournal: J.Virol. / Year: 2015
Title: Nanobody binding to a conserved epitope promotes norovirus particle disassembly.
Authors: Koromyslova, A.D. / Hansman, G.S.
History
DepositionDec 9, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 31, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 14, 2015Group: Database references
Revision 1.2Feb 18, 2015Group: Database references
Revision 1.3Apr 10, 2019Group: Data collection / Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_variant
Revision 1.4Jan 10, 2024Group: 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Capsid protein
B: Capsid protein
C: Nano-25 Nanobody
D: Nano-25 Nanobody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,01431
Polymers95,3314
Non-polymers1,68427
Water8,359464
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13600 Å2
ΔGint42 kcal/mol
Surface area30080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.280, 112.980, 142.890
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
11chain A
21chain B
12chain C
22chain D

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYSMETMETchain AAA225 - 5382 - 315
21SERSERMETMETchain BBB224 - 5381 - 315
12ASPASPHISHISchain CCC1 - 1141 - 114
22ASPASPSERSERchain DDD1 - 1121 - 112

NCS ensembles :
ID
1
2
DetailsThe biological unit is a dimer. There is 1 biological unit in the asymmetric unit (chains A & B)

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Components

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Protein / Antibody , 2 types, 4 molecules ABCD

#1: Protein Capsid protein


Mass: 34506.660 Da / Num. of mol.: 2 / Fragment: VHH, UNP residues 224-538
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Norwalk virus / Plasmid: pMBP / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q5F4T5
#2: Antibody Nano-25 Nanobody


Mass: 13158.593 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca) / Plasmid: pHEN6C / Production host: Escherichia coli (E. coli) / Variant (production host): WK6

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Non-polymers , 5 types, 491 molecules

#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5N2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 464 / Source method: isolated from a natural source / Formula: H2O

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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: 2.02 Å3/Da / Density % sol: 39.11 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: PEG3350, ammonium dihydrogen phosphate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.984 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 9, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.984 Å / Relative weight: 1
ReflectionResolution: 1.7→46.59 Å / Num. obs: 88133 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 4.7 % / Biso Wilson estimate: 24.11 Å2 / Rmerge F obs: 0.997 / Rmerge(I) obs: 0.056 / Rrim(I) all: 0.067 / Χ2: 0.988 / Net I/σ(I): 14.33 / Num. measured all: 412753
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.7-1.83.60.7510.3552.582075512512111780.48796.8
1.74-1.790.8630.2972.422834912289119990.37497.6
1.79-1.840.9030.2433.313076011878117310.398.8
1.84-1.90.9380.1944.143004411678115190.2498.6
1.9-1.960.9630.1495.322848611178110240.18498.6
1.96-2.030.9740.1196.432602510868106800.14998.3
2.03-2.110.9790.1067.982674810416102410.1398.3
2.11-2.190.9820.0969.182666810162100020.11798.4
2.19-2.290.9860.08510.3124685961994230.10498
2.29-2.40.9880.07711.3622971924790280.09597.6
2.4-2.530.9890.07112.1421026877785450.08897.4
2.53-2.690.9920.06513.9221667835881710.0897.8
2.69-2.870.9920.0615.2719823782276660.07498
2.87-3.10.9940.05316.5217711728871470.06598.1
3.1-3.40.9930.04817.7615581668665480.0697.9
3.4-3.80.9950.04419.4814832605659090.05497.6
3.8-4.390.9950.04219.8212683532752630.05298.8
4.39-5.370.9950.03919.9110418451444050.04997.6
5.37-7.60.9970.03620.828806347633190.04495.5
7.60.9970.03120.824715192118910.03898.4

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Processing

Software
NameVersionClassification
XDSdata reduction
PHENIXrefinement
PDB_EXTRACT3.15data extraction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: As search models for molecular replacement PDB code 3ONU was used for GII.10 P domain (molecule 1) and PDB code 3P0G for Nano-25 (molecule 2)
Resolution: 1.7→46.587 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.09 / Phase error: 17.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1868 8313 5.02 %
Rwork0.1599 157298 -
obs0.1612 88133 97.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 94.62 Å2 / Biso mean: 32.6161 Å2 / Biso min: 13.2 Å2
Refinement stepCycle: final / Resolution: 1.7→46.587 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6330 0 108 464 6902
Biso mean--42.22 38.57 -
Num. residues----836
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016614
X-RAY DIFFRACTIONf_angle_d1.1918997
X-RAY DIFFRACTIONf_chiral_restr0.061001
X-RAY DIFFRACTIONf_plane_restr0.0071182
X-RAY DIFFRACTIONf_dihedral_angle_d12.4682323
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2724X-RAY DIFFRACTION5.986TORSIONAL
12B2724X-RAY DIFFRACTION5.986TORSIONAL
21C936X-RAY DIFFRACTION5.986TORSIONAL
22D936X-RAY DIFFRACTION5.986TORSIONAL
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6984-1.71770.29192310.27634407X-RAY DIFFRACTION83
1.7177-1.73790.28512750.25495116X-RAY DIFFRACTION95
1.7379-1.75910.27732760.23825195X-RAY DIFFRACTION96
1.7591-1.78140.25912740.21895223X-RAY DIFFRACTION98
1.7814-1.80480.25162850.20525351X-RAY DIFFRACTION99
1.8048-1.82960.20592780.18135328X-RAY DIFFRACTION99
1.8296-1.85570.22032790.18095267X-RAY DIFFRACTION99
1.8557-1.88340.21322830.16915335X-RAY DIFFRACTION99
1.8834-1.91280.18632790.16895287X-RAY DIFFRACTION98
1.9128-1.94420.20742800.1625311X-RAY DIFFRACTION99
1.9442-1.97770.20732860.16495342X-RAY DIFFRACTION98
1.9777-2.01370.17752700.15895242X-RAY DIFFRACTION98
2.0137-2.05240.19222850.15315370X-RAY DIFFRACTION98
2.0524-2.09430.1882790.15665241X-RAY DIFFRACTION98
2.0943-2.13980.19282780.15595344X-RAY DIFFRACTION99
2.1398-2.18960.19292740.1525236X-RAY DIFFRACTION98
2.1896-2.24440.17242800.15595333X-RAY DIFFRACTION98
2.2444-2.30510.17612750.1565237X-RAY DIFFRACTION98
2.3051-2.37290.19492760.15565249X-RAY DIFFRACTION98
2.3729-2.44950.18772740.15625254X-RAY DIFFRACTION97
2.4495-2.5370.18742740.15785230X-RAY DIFFRACTION98
2.537-2.63860.20542770.15775276X-RAY DIFFRACTION98
2.6386-2.75870.19512810.15595264X-RAY DIFFRACTION98
2.7587-2.90410.19992820.16075310X-RAY DIFFRACTION98
2.9041-3.0860.20282800.15865272X-RAY DIFFRACTION98
3.086-3.32420.17592780.1565252X-RAY DIFFRACTION98
3.3242-3.65860.16512760.14655241X-RAY DIFFRACTION98
3.6586-4.18770.15362810.14545324X-RAY DIFFRACTION98
4.1877-5.27490.15082850.14015262X-RAY DIFFRACTION98
5.2749-46.60470.20972820.18295199X-RAY DIFFRACTION97
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)
11.4665-0.5309-0.28171.4668-0.56181.72630.0219-0.26610.02710.05340.04070.0639-0.10720.123-0.05870.1235-0.0379-0.00420.1921-0.01120.13643.682-4.6621-21.8344
21.3077-0.15690.18330.8426-0.65372.28580.0544-0.10750.19890.12910.04310.1043-0.5627-0.0731-0.06990.26580.01120.06110.1332-0.03370.2053-2.68549.5125-26.6297
31.8728-1.2735-1.21731.93570.34412.55190.2353-0.54470.12290.6368-0.1170.3207-0.4441-0.0979-0.0660.2794-0.01240.0450.3487-0.01530.21081.5508-1.9688-10.7192
41.0711-0.1072-0.31290.9186-0.71221.73990.0307-0.3692-0.05930.0542-0.0635-0.1877-0.04410.3980.01250.1372-0.0308-0.02010.32260.03790.167714.7539-8.6294-19.586
55.08322.5531-1.51712.5323-1.16472.325-0.0106-0.3016-0.3685-0.3585-0.3141-0.34020.28240.94110.30340.31170.07160.02450.50480.13310.336421.3422-23.9847-22.619
62.530.1759-0.49542.1037-0.15191.5993-0.0654-0.0322-0.06840.108-0.1151-0.36990.0260.90930.07320.1582-0.0381-0.03630.58330.12910.245123.5536-15.2886-17.4735
71.87850.48810.62842.3017-1.9174.3410.2154-0.3659-0.3284-0.138-0.167-0.24540.40840.7263-0.04220.24550.07880.02390.48770.11140.319422.5102-24.6564-16.3733
82.06850.1115-0.56421.03420.85562.00770.03220.01860.0326-0.1279-0.03260.0370.0377-0.0552-0.0030.1951-0-0.00620.11790.01150.16282.907-11.0003-45.6493
91.69111.1238-0.1554.3229-0.12751.20980.1-0.12310.1185-0.095-0.033-0.1357-0.18280.267-0.09740.1587-0.04050.02150.182-0.00310.197717.0882-3.073-41.6886
101.42680.7342-0.02112.9197-0.01742.52360.12220.09950.2657-0.0767-0.1104-0.4185-0.49870.3507-0.04670.289-0.11290.07320.3269-0.02420.386622.71627.4535-41.3893
111.01720.0985-0.44951.58720.52882.17570.2472-0.20250.2019-0.0757-0.0877-0.2862-0.55190.3825-0.10130.2946-0.10580.06550.2003-0.02020.254616.74477.8188-41.5247
121.67710.3316-0.26941.5936-0.20271.4670.2268-0.06170.3195-0.2128-0.0821-0.2157-0.54870.1887-0.070.3224-0.05810.08830.1335-0.01360.254512.44068.0134-46.2111
130.87270.231-0.31870.40970.59781.25760.05860.0354-0.0363-0.0502-0.0360.0391-0.0081-0.0587-0.04050.197-0.0087-0.00110.1261-0.00180.18482.8183-9.0994-47.0485
144.2137-1.21540.42473.76310.20492.4849-0.0919-0.1732-0.17830.12880.01520.40970.1425-0.32050.08160.2291-0.0198-0.0070.1633-0.01240.2251-2.2092-20.5596-47.9641
151.1832-0.3082-0.19570.87950.85612.4251-0.13450.04-0.10860.03740.05310.04760.4124-0.18610.06590.2848-0.03720.00960.1790.00080.2545-1.3906-25.785-51.3771
164.1957-2.47142.45074.8296-1.30825.888-0.1645-0.2533-0.0133-0.04370.0249-0.211-0.50640.32420.15770.42950.0503-0.12390.7348-0.03440.399810.7543-11.57796.5807
171.8656-1.67371.19591.6939-0.47192.0495-0.1903-0.5326-0.28540.44020.42480.2377-0.2159-0.554-0.12530.3530.07690.02160.80490.25070.395611.69-26.628615.2275
183.06261.03520.77927.14815.30873.9571-0.1977-0.08220.17180.31760.08890.3433-0.1158-0.00480.10720.27460.06390.01830.42270.090.2384.3983-14.009-2.2081
197.6565-2.50913.99674.0084-2.92397.98530.34170.06470.22080.0809-0.4647-0.17260.00530.34490.01910.2721-0.0721-0.05520.47850.11490.228915.8619-21.1873.0679
203.79291.12531.90013.25711.42333.60320.18040.0546-0.1490.1394-0.0952-0.6353-0.03260.881-0.0370.1596-0.0274-0.22880.90020.31330.200820.5297-22.8733.3152
213.9523-4.23131.18467.0438-1.53851.20520.18550.4502-0.1721-0.9226-0.1350.9001-0.1474-0.06290.01560.4742-0.0809-0.21170.51460.14450.45758.328-27.4247-4.183
222.4324-1.34780.62083.155-0.45611.1510.4277-0.2393-0.2631-0.4329-0.01750.4361-0.0643-0.3009-0.33690.3199-0.0205-0.05010.57940.2420.45639.1426-28.07834.2124
233.41280.4352.72191.6479-1.0774.02950.1839-0.1357-0.54540.03290.17930.06940.32560.0606-0.27290.2834-0.0605-0.03840.71440.22820.3314.4175-29.481511.0551
240.6784-1.05650.61151.7784-1.24311.6128-0.2334-0.2939-0.01250.52730.2455-0.0854-0.4796-0.22350.02970.34220.0133-0.08720.66590.07650.280817.8267-19.02919.7463
252.98911.58631.48788.05183.20663.6368-0.33920.7411-0.1858-0.33480.2055-0.1571-0.3444-0.17090.15120.3798-0.09460.09230.4309-0.06790.23838.1274-19.8707-80.1418
265.66981.3348-1.29663.3453-3.22883.14070.1726-0.10260.6249-0.05590.1164-0.1041-0.90920.6139-0.24860.3931-0.07890.03490.3157-0.08080.319413.2672-11.1287-64.459
275.01291.06611.58553.23720.78094.1861-0.20750.22760.0969-0.28670.03670.3116-0.1174-0.42290.13640.2187-0.0171-0.00660.2139-0.02980.1731.4071-21.6066-70.5187
285.77930.6471.03852.8120.85015.1951-0.2294-0.3353-0.42320.28590.1105-0.08570.47380.26940.12320.29930.01890.06950.2049-0.02770.346810.533-27.2437-68.519
292.9970.06870.08872.20840.67514.056-0.23470.6406-0.278-0.28150.0439-0.0244-0.1565-0.28940.15940.2578-0.04930.04370.3193-0.06670.20295.0808-20.8015-76.1196
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 225 through 332 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 333 through 406 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 407 through 427 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 428 through 472 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 473 through 492 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 493 through 521 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 522 through 538 )A0
8X-RAY DIFFRACTION8chain 'B' and (resid 224 through 265 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 266 through 294 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 298 through 317 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 318 through 379 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 380 through 426 )B0
13X-RAY DIFFRACTION13chain 'B' and (resid 427 through 472 )B0
14X-RAY DIFFRACTION14chain 'B' and (resid 473 through 520 )B0
15X-RAY DIFFRACTION15chain 'B' and (resid 521 through 538 )B0
16X-RAY DIFFRACTION16chain 'C' and (resid 1 through 7 )C0
17X-RAY DIFFRACTION17chain 'C' and (resid 8 through 24 )C0
18X-RAY DIFFRACTION18chain 'C' and (resid 25 through 32 )C0
19X-RAY DIFFRACTION19chain 'C' and (resid 33 through 39 )C0
20X-RAY DIFFRACTION20chain 'C' and (resid 40 through 52 )C0
21X-RAY DIFFRACTION21chain 'C' and (resid 53 through 59 )C0
22X-RAY DIFFRACTION22chain 'C' and (resid 60 through 76 )C0
23X-RAY DIFFRACTION23chain 'C' and (resid 77 through 90 )C0
24X-RAY DIFFRACTION24chain 'C' and (resid 91 through 114 )C0
25X-RAY DIFFRACTION25chain 'D' and (resid 1 through 24 )D0
26X-RAY DIFFRACTION26chain 'D' and (resid 25 through 32 )D0
27X-RAY DIFFRACTION27chain 'D' and (resid 33 through 52 )D0
28X-RAY DIFFRACTION28chain 'D' and (resid 53 through 72 )D0
29X-RAY DIFFRACTION29chain 'D' and (resid 73 through 112 )D0

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