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- PDB-4v5v: Structure of respiratory syncytial virus nucleocapsid protein, P1... -

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Basic information

Entry
Database: PDB / ID: 4v5v
TitleStructure of respiratory syncytial virus nucleocapsid protein, P1 crystal form
Components
  • RESPIRATORY SYNCYTIAL VIRUS NUCLEOCAPSID PROTEIN
  • RNA
KeywordsVIRAL PROTEIN/RNA / VIRAL PROTEIN-RNA COMPLEX
Function / homology
Function and homology information


symbiont-mediated suppression of host PKR/eIFalpha signaling / helical viral capsid / viral nucleocapsid / host cell cytoplasm / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / RNA binding / cytoplasm
Similarity search - Function
Pneumovirus nucleocapsid protein / Pneumovirus nucleocapsid protein
Similarity search - Domain/homology
RNA / RNA (> 10) / Nucleoprotein
Similarity search - Component
Biological speciesHUMAN RESPIRATORY SYNCYTIAL VIRUS
ESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.6 Å
AuthorsEl Omari, K. / Dhaliwal, B. / Ren, J. / Abrescia, N.G.A. / Lockyer, M. / Powell, K.L. / Hawkins, A.R. / Stammers, D.K.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2011
Title: Structures of Respiratory Syncytial Virus Nucleocapsid Protein from Two Crystal Forms: Details of Potential Packing Interactions in the Native Helical Form.
Authors: El Omari, K. / Dhaliwal, B. / Ren, J. / Abrescia, N.G.A. / Lockyer, M. / Powell, K.L. / Hawkins, A.R. / Stammers, D.K.
History
DepositionMay 4, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 9, 2014Provider: repository / Type: Initial release
SupersessionDec 10, 2014ID: 2YHP, 2YHQ
Revision 1.1Dec 10, 2014Group: Other
Revision 1.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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
AA: RESPIRATORY SYNCYTIAL VIRUS NUCLEOCAPSID PROTEIN
AB: RESPIRATORY SYNCYTIAL VIRUS NUCLEOCAPSID PROTEIN
AC: RESPIRATORY SYNCYTIAL VIRUS NUCLEOCAPSID PROTEIN
AD: RESPIRATORY SYNCYTIAL VIRUS NUCLEOCAPSID PROTEIN
AE: RESPIRATORY SYNCYTIAL VIRUS NUCLEOCAPSID PROTEIN
AF: RESPIRATORY SYNCYTIAL VIRUS NUCLEOCAPSID PROTEIN
AG: RESPIRATORY SYNCYTIAL VIRUS NUCLEOCAPSID PROTEIN
AH: RESPIRATORY SYNCYTIAL VIRUS NUCLEOCAPSID PROTEIN
AI: RESPIRATORY SYNCYTIAL VIRUS NUCLEOCAPSID PROTEIN
AJ: RESPIRATORY SYNCYTIAL VIRUS NUCLEOCAPSID PROTEIN
AK: RNA
AL: RESPIRATORY SYNCYTIAL VIRUS NUCLEOCAPSID PROTEIN
AM: RNA
AN: RESPIRATORY SYNCYTIAL VIRUS NUCLEOCAPSID PROTEIN
AO: RESPIRATORY SYNCYTIAL VIRUS NUCLEOCAPSID PROTEIN
AP: RESPIRATORY SYNCYTIAL VIRUS NUCLEOCAPSID PROTEIN
AQ: RESPIRATORY SYNCYTIAL VIRUS NUCLEOCAPSID PROTEIN
AR: RESPIRATORY SYNCYTIAL VIRUS NUCLEOCAPSID PROTEIN
AS: RESPIRATORY SYNCYTIAL VIRUS NUCLEOCAPSID PROTEIN
AT: RESPIRATORY SYNCYTIAL VIRUS NUCLEOCAPSID PROTEIN
AU: RESPIRATORY SYNCYTIAL VIRUS NUCLEOCAPSID PROTEIN
AV: RESPIRATORY SYNCYTIAL VIRUS NUCLEOCAPSID PROTEIN
BA: RESPIRATORY SYNCYTIAL VIRUS NUCLEOCAPSID PROTEIN
BB: RESPIRATORY SYNCYTIAL VIRUS NUCLEOCAPSID PROTEIN
BC: RESPIRATORY SYNCYTIAL VIRUS NUCLEOCAPSID PROTEIN
BD: RESPIRATORY SYNCYTIAL VIRUS NUCLEOCAPSID PROTEIN
BE: RESPIRATORY SYNCYTIAL VIRUS NUCLEOCAPSID PROTEIN
BF: RESPIRATORY SYNCYTIAL VIRUS NUCLEOCAPSID PROTEIN
BG: RESPIRATORY SYNCYTIAL VIRUS NUCLEOCAPSID PROTEIN
BH: RESPIRATORY SYNCYTIAL VIRUS NUCLEOCAPSID PROTEIN
BI: RESPIRATORY SYNCYTIAL VIRUS NUCLEOCAPSID PROTEIN
BJ: RESPIRATORY SYNCYTIAL VIRUS NUCLEOCAPSID PROTEIN
BK: RESPIRATORY SYNCYTIAL VIRUS NUCLEOCAPSID PROTEIN
BL: RESPIRATORY SYNCYTIAL VIRUS NUCLEOCAPSID PROTEIN
BM: RESPIRATORY SYNCYTIAL VIRUS NUCLEOCAPSID PROTEIN
BN: RESPIRATORY SYNCYTIAL VIRUS NUCLEOCAPSID PROTEIN
BO: RESPIRATORY SYNCYTIAL VIRUS NUCLEOCAPSID PROTEIN
BP: RESPIRATORY SYNCYTIAL VIRUS NUCLEOCAPSID PROTEIN
BQ: RESPIRATORY SYNCYTIAL VIRUS NUCLEOCAPSID PROTEIN
BR: RNA
BW: RESPIRATORY SYNCYTIAL VIRUS NUCLEOCAPSID PROTEIN
BX: RNA
BY: RESPIRATORY SYNCYTIAL VIRUS NUCLEOCAPSID PROTEIN
BZ: RESPIRATORY SYNCYTIAL VIRUS NUCLEOCAPSID PROTEIN


Theoretical massNumber of molelcules
Total (without water)1,751,66444
Polymers1,751,66444
Non-polymers00
Water0
1
AA: RESPIRATORY SYNCYTIAL VIRUS NUCLEOCAPSID PROTEIN
AB: RESPIRATORY SYNCYTIAL VIRUS NUCLEOCAPSID PROTEIN
AC: RESPIRATORY SYNCYTIAL VIRUS NUCLEOCAPSID PROTEIN
AD: RESPIRATORY SYNCYTIAL VIRUS NUCLEOCAPSID PROTEIN
AE: RESPIRATORY SYNCYTIAL VIRUS NUCLEOCAPSID PROTEIN
AF: RESPIRATORY SYNCYTIAL VIRUS NUCLEOCAPSID PROTEIN
AG: RESPIRATORY SYNCYTIAL VIRUS NUCLEOCAPSID PROTEIN
AH: RESPIRATORY SYNCYTIAL VIRUS NUCLEOCAPSID PROTEIN
AI: RESPIRATORY SYNCYTIAL VIRUS NUCLEOCAPSID PROTEIN
AJ: RESPIRATORY SYNCYTIAL VIRUS NUCLEOCAPSID PROTEIN
AK: RNA


Theoretical massNumber of molelcules
Total (without water)437,91611
Polymers437,91611
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area72620 Å2
ΔGint-446.4 kcal/mol
Surface area150930 Å2
MethodPISA
2
AL: RESPIRATORY SYNCYTIAL VIRUS NUCLEOCAPSID PROTEIN
AM: RNA
AN: RESPIRATORY SYNCYTIAL VIRUS NUCLEOCAPSID PROTEIN
AO: RESPIRATORY SYNCYTIAL VIRUS NUCLEOCAPSID PROTEIN
AP: RESPIRATORY SYNCYTIAL VIRUS NUCLEOCAPSID PROTEIN
AQ: RESPIRATORY SYNCYTIAL VIRUS NUCLEOCAPSID PROTEIN
AR: RESPIRATORY SYNCYTIAL VIRUS NUCLEOCAPSID PROTEIN
AS: RESPIRATORY SYNCYTIAL VIRUS NUCLEOCAPSID PROTEIN
AT: RESPIRATORY SYNCYTIAL VIRUS NUCLEOCAPSID PROTEIN
AU: RESPIRATORY SYNCYTIAL VIRUS NUCLEOCAPSID PROTEIN
AV: RESPIRATORY SYNCYTIAL VIRUS NUCLEOCAPSID PROTEIN


Theoretical massNumber of molelcules
Total (without water)437,91611
Polymers437,91611
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area72630 Å2
ΔGint-445.8 kcal/mol
Surface area150860 Å2
MethodPISA
3
BA: RESPIRATORY SYNCYTIAL VIRUS NUCLEOCAPSID PROTEIN
BB: RESPIRATORY SYNCYTIAL VIRUS NUCLEOCAPSID PROTEIN
BC: RESPIRATORY SYNCYTIAL VIRUS NUCLEOCAPSID PROTEIN
BD: RESPIRATORY SYNCYTIAL VIRUS NUCLEOCAPSID PROTEIN
BE: RESPIRATORY SYNCYTIAL VIRUS NUCLEOCAPSID PROTEIN
BF: RESPIRATORY SYNCYTIAL VIRUS NUCLEOCAPSID PROTEIN
BG: RESPIRATORY SYNCYTIAL VIRUS NUCLEOCAPSID PROTEIN
BH: RESPIRATORY SYNCYTIAL VIRUS NUCLEOCAPSID PROTEIN
BI: RESPIRATORY SYNCYTIAL VIRUS NUCLEOCAPSID PROTEIN
BQ: RESPIRATORY SYNCYTIAL VIRUS NUCLEOCAPSID PROTEIN
BR: RNA


Theoretical massNumber of molelcules
Total (without water)437,91611
Polymers437,91611
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area72070 Å2
ΔGint-444 kcal/mol
Surface area151480 Å2
MethodPISA
4
BJ: RESPIRATORY SYNCYTIAL VIRUS NUCLEOCAPSID PROTEIN
BK: RESPIRATORY SYNCYTIAL VIRUS NUCLEOCAPSID PROTEIN
BL: RESPIRATORY SYNCYTIAL VIRUS NUCLEOCAPSID PROTEIN
BM: RESPIRATORY SYNCYTIAL VIRUS NUCLEOCAPSID PROTEIN
BN: RESPIRATORY SYNCYTIAL VIRUS NUCLEOCAPSID PROTEIN
BO: RESPIRATORY SYNCYTIAL VIRUS NUCLEOCAPSID PROTEIN
BP: RESPIRATORY SYNCYTIAL VIRUS NUCLEOCAPSID PROTEIN
BW: RESPIRATORY SYNCYTIAL VIRUS NUCLEOCAPSID PROTEIN
BX: RNA
BY: RESPIRATORY SYNCYTIAL VIRUS NUCLEOCAPSID PROTEIN
BZ: RESPIRATORY SYNCYTIAL VIRUS NUCLEOCAPSID PROTEIN


Theoretical massNumber of molelcules
Total (without water)437,91611
Polymers437,91611
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area72110 Å2
ΔGint-445 kcal/mol
Surface area151440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)164.347, 175.740, 241.977
Angle α, β, γ (deg.)90.09, 89.96, 89.92
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11AA
21AB
31AC
41AD
51AE
61AF
71AG
81AH
91AI
101AJ
111AL
121AN
131AO
141AP
151AQ
161AR
171AS
181AT
191AU
201AV
211BW
221BY
231BZ
241BJ
251BK
261BL
271BM
281BN
291BO
301BP
311BQ
321BI
331BA
341BB
351BC
361BD
371BE
381BF
391BG
401BH

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 1 / Auth seq-ID: 1 - 375 / Label seq-ID: 1 - 375

Dom-IDAuth asym-IDLabel asym-ID
1AAA
2ABB
3ACC
4ADD
5AEE
6AFF
7AGG
8AHH
9AII
10AJJ
11ALL
12ANN
13AOO
14APP
15AQQ
16ARR
17ASS
18ATT
19AUU
20AVV
21BWOA
22BYQA
23BZRA
24BJFA
25BKGA
26BLHA
27BMIA
28BNJA
29BOKA
30BPLA
31BQMA
32BIEA
33BAW
34BBX
35BCY
36BDZ
37BEAA
38BFBA
39BGCA
40BHDA

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Components

#1: Protein ...
RESPIRATORY SYNCYTIAL VIRUS NUCLEOCAPSID PROTEIN


Mass: 41659.820 Da / Num. of mol.: 40 / Fragment: RESIDUES 1-375
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HUMAN RESPIRATORY SYNCYTIAL VIRUS / Strain: STRAIN A / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q4KRW9
#2: RNA chain
RNA /


Mass: 21317.777 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Details: NON SPECIFIC RNA FROM CELLULAR ORIGIN BOUND TO THE NUCLEOPROTEIN
Source: (natural) ESCHERICHIA COLI (E. coli)

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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: 3.99 Å3/Da / Density % sol: 69 % / Description: NONE
Crystal growpH: 7.5
Details: 10% (V/V) MPD, 0.05 M AMMONIUM ACETATE, 0.05 M TRIS PH7.5, 0.01 M MGCL2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9797
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionResolution: 3.6→50 Å / Num. obs: 330486 / % possible obs: 97.3 % / Observed criterion σ(I): 1.2 / Redundancy: 1.9 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 6.7
Reflection shellResolution: 3.6→3.73 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 1.2 / % possible all: 97.7

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Processing

Software
NameVersionClassification
MOLREPmodel building
REFMAC5.6.0070refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WJ8
Resolution: 3.6→50 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.933 / SU B: 44.873 / SU ML: 0.589 / Cross valid method: THROUGHOUT / ESU R Free: 0.647 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT.
RfactorNum. reflection% reflectionSelection details
Rfree0.269 15380 5 %RANDOM
Rwork0.234 ---
obs0.236 289510 97.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 146.03 Å2
Baniso -1Baniso -2Baniso -3
1-19.77 Å20.51 Å2-0.2 Å2
2---8.9 Å20.92 Å2
3----10.87 Å2
Refinement stepCycle: LAST / Resolution: 3.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms58400 2800 0 0 61200
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.021124876
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2731.941169424
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.025514960
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.86124.5045240
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.1671521880
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.55715640
X-RAY DIFFRACTIONr_chiral_restr0.0880.219160
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0290360
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 2912 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1AAtight positional0.020.05
2ABtight positional0.020.05
3ACtight positional0.020.05
4ADtight positional0.020.05
5AEtight positional0.020.05
6AFtight positional0.020.05
7AGtight positional0.020.05
8AHtight positional0.020.05
9AItight positional0.030.05
10AJtight positional0.020.05
11ALtight positional0.020.05
12ANtight positional0.020.05
13AOtight positional0.020.05
14APtight positional0.020.05
15AQtight positional0.030.05
16ARtight positional0.020.05
17AStight positional0.020.05
18ATtight positional0.020.05
19AUtight positional0.020.05
20AVtight positional0.020.05
21BWtight positional0.020.05
22BYtight positional0.020.05
23BZtight positional0.020.05
24BJtight positional0.030.05
25BKtight positional0.020.05
26BLtight positional0.030.05
27BMtight positional0.020.05
28BNtight positional0.020.05
29BOtight positional0.030.05
30BPtight positional0.020.05
31BQtight positional0.030.05
32BItight positional0.020.05
33BAtight positional0.020.05
34BBtight positional0.020.05
35BCtight positional0.020.05
36BDtight positional0.020.05
37BEtight positional0.020.05
38BFtight positional0.020.05
39BGtight positional0.020.05
40BHtight positional0.020.05
1AAtight thermal15.470.5
2ABtight thermal16.480.5
3ACtight thermal15.190.5
4ADtight thermal17.260.5
5AEtight thermal14.850.5
6AFtight thermal15.730.5
7AGtight thermal21.170.5
8AHtight thermal15.540.5
9AItight thermal15.990.5
10AJtight thermal15.590.5
11ALtight thermal14.940.5
12ANtight thermal23.280.5
13AOtight thermal16.460.5
14APtight thermal15.570.5
15AQtight thermal15.850.5
16ARtight thermal16.470.5
17AStight thermal15.180.5
18ATtight thermal14.970.5
19AUtight thermal15.970.5
20AVtight thermal16.070.5
21BWtight thermal14.990.5
22BYtight thermal17.540.5
23BZtight thermal14.290.5
24BJtight thermal16.420.5
25BKtight thermal15.780.5
26BLtight thermal14.810.5
27BMtight thermal15.120.5
28BNtight thermal14.630.5
29BOtight thermal15.630.5
30BPtight thermal15.880.5
31BQtight thermal150.5
32BItight thermal15.060.5
33BAtight thermal14.910.5
34BBtight thermal14.780.5
35BCtight thermal15.080.5
36BDtight thermal15.680.5
37BEtight thermal150.5
38BFtight thermal17.240.5
39BGtight thermal14.320.5
40BHtight thermal15.630.5
LS refinement shellResolution: 3.6→3.69 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.462 1167 -
Rwork0.456 21463 -
obs--97.93 %

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