[English] 日本語
Yorodumi
- PDB-5t1d: Crystal structure of EBV gHgL/gp42/E1D1 complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5t1d
TitleCrystal structure of EBV gHgL/gp42/E1D1 complex
Components
  • (Envelope glycoprotein ...) x 2
  • E1D1 IgG2a heavy chain
  • E1D1 IgG2a light chain
  • Glycoprotein 42
KeywordsVIRAL PROTEIN / receptor binding / herpesvirus entry / Epstein-Barr Virus / membrane fusion
Function / homology
Function and homology information


host cell endosome membrane / carbohydrate binding / host cell Golgi apparatus / fusion of virus membrane with host plasma membrane / viral envelope / symbiont entry into host cell / host cell plasma membrane / virion membrane / membrane
Similarity search - Function
Viral glycoprotein L / Herpesvirus glycoprotein H, domain D-II / SAND domain / Herpesvirus glycoprotein L, rhadinovirus-type / Herpesvirus glycoprotein L, rhadinovirus-type superfamily / Viral glycoprotein L / Envelope glycoprotein L / Herpesvirus glycoprotein H main domain / Herpesvirus glycoprotein H / Herpesvirus glycoprotein H, C-terminal ...Viral glycoprotein L / Herpesvirus glycoprotein H, domain D-II / SAND domain / Herpesvirus glycoprotein L, rhadinovirus-type / Herpesvirus glycoprotein L, rhadinovirus-type superfamily / Viral glycoprotein L / Envelope glycoprotein L / Herpesvirus glycoprotein H main domain / Herpesvirus glycoprotein H / Herpesvirus glycoprotein H, C-terminal / Herpesvirus glycoprotein H, C-terminal domain superfamily / Herpesvirus glycoprotein H C-terminal domain / Naphthalene 1,2-dioxygenase Alpha Subunit; Chain A, domain 1 / C-type lectin-like/link domain superfamily / C-type lectin fold / Roll / Immunoglobulins / Alpha-Beta Complex / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Envelope glycoprotein L / Envelope glycoprotein H / Glycoprotein 42
Similarity search - Component
Biological speciesEpstein-Barr virus (Epstein-Barr virus)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.1 Å
AuthorsSathiyamoorthy, K. / Jardetzky, T.S.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI119480 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI076183 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CA117794 United States
CitationJournal: Nat Commun / Year: 2016
Title: Structural basis for Epstein-Barr virus host cell tropism mediated by gp42 and gHgL entry glycoproteins.
Authors: Sathiyamoorthy, K. / Hu, Y.X. / Mohl, B.S. / Chen, J. / Longnecker, R. / Jardetzky, T.S.
History
DepositionAug 18, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 28, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 4, 2017Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Envelope glycoprotein H
B: Envelope glycoprotein L
C: Glycoprotein 42
H: E1D1 IgG2a heavy chain
L: E1D1 IgG2a light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,3777
Polymers153,5285
Non-polymers8492
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)105.510, 166.000, 272.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

-
Components

-
Envelope glycoprotein ... , 2 types, 2 molecules AB

#1: Protein Envelope glycoprotein H / gH


Mass: 72600.352 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Epstein-Barr virus (strain B95-8) (Epstein-Barr virus (strain B95-8))
Strain: B95-8 / Gene: gH, BXLF2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P03231
#2: Protein Envelope glycoprotein L / gL


Mass: 12475.127 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Epstein-Barr virus (strain B95-8) (Epstein-Barr virus (strain B95-8))
Strain: B95-8 / Gene: gL, BKRF2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P03212

-
Antibody , 2 types, 2 molecules HL

#4: Antibody E1D1 IgG2a heavy chain


Mass: 22839.424 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell line: E1D1 hybridoma
#5: Antibody E1D1 IgG2a light chain


Mass: 23986.654 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell line: E1D1 hybridoma

-
Protein / Sugars , 2 types, 3 molecules C

#3: Protein Glycoprotein 42 / gp42


Mass: 21626.496 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Epstein-Barr virus (strain GD1) (Epstein-Barr virus)
Strain: GD1 / Gene: BZLF2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P0C6Z5
#6: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.88 Å3/Da / Density % sol: 68.33 %
Description: Slender rod-shaped crystals, initial crystals in PEG 3350 and different citrates resembles the pattern of a cracked tree bark slab
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1 M Tris pH 8.0, 0.18 M Potassium Citrate, 12 % PEG 6000
Temp details: Room temperature

-
Data collection

DiffractionMean temperature: 100 K / Ambient temp details: cryostream
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 29, 2015
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.901→46.11 Å / Num. obs: 53195 / % possible obs: 99.83 % / Redundancy: 5.9 % / Biso Wilson estimate: 77.97 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.1232 / Net I/σ(I): 12.21
Reflection shellResolution: 2.901→3.005 Å / Redundancy: 5.9 % / Rmerge(I) obs: 1.59 / Mean I/σ(I) obs: 1.6 / CC1/2: 0.586 / % possible all: 99.05

-
Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementResolution: 3.1→46.11 Å / SU ML: 0.41 / σ(F): 1.36 / Phase error: 26.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.265 1977 4.98 %
Rwork0.2116 --
obs0.2143 39681 90.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.1→46.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10554 0 56 0 10610
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00410893
X-RAY DIFFRACTIONf_angle_d0.63414823
X-RAY DIFFRACTIONf_dihedral_angle_d11.7026460
X-RAY DIFFRACTIONf_chiral_restr0.0421693
X-RAY DIFFRACTIONf_plane_restr0.0041865
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.17750.3738870.30041776X-RAY DIFFRACTION60
3.1775-3.26340.34051070.29031918X-RAY DIFFRACTION66
3.2634-3.35940.29621110.28742189X-RAY DIFFRACTION74
3.3594-3.46780.3041290.26262361X-RAY DIFFRACTION81
3.4678-3.59170.31611350.24282630X-RAY DIFFRACTION89
3.5917-3.73550.29721470.23692866X-RAY DIFFRACTION97
3.7355-3.90540.26671530.22052959X-RAY DIFFRACTION100
3.9054-4.11120.27391570.20752942X-RAY DIFFRACTION100
4.1112-4.36860.26641540.18522955X-RAY DIFFRACTION100
4.3686-4.70550.18281570.16262966X-RAY DIFFRACTION100
4.7055-5.17850.23181600.16612982X-RAY DIFFRACTION100
5.1785-5.92650.29161550.19123003X-RAY DIFFRACTION100
5.9265-7.46170.2551590.22513025X-RAY DIFFRACTION100
7.4617-46.11480.24351660.20113132X-RAY DIFFRACTION100
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.70761.2941.69544.7356-0.46043.1691-0.0006-0.27530.73720.2458-0.144-0.0584-0.53370.3480.140.2475-0.0973-0.01350.5603-0.28430.8186258.3115219.2246583.7055
22.3553-0.05161.23392.9156-0.70152.4354-0.17920.11030.5802-0.08920.2583-0.164-0.2545-0.14730.03930.2953-0.10420.07560.3066-0.14380.3567232.3644215.557572.1086
33.2835-0.94331.65861.7321-0.76343.22620.13360.27040.2813-0.2170.1644-0.58760.34230.253-0.15760.2186-0.0127-0.01570.2135-0.29780.0517237.8375201.7858572.3379
42.84731.13370.87912.48290.07291.78450.1381-0.14220.316-0.1548-0.00490.00510.11730.0989-0.01120.29710.0234-0.0790.1473-0.0186-0.1101212.3205197.2615562.4824
54.82450.49410.13175.3064-1.37833.83430.3638-0.1548-0.23580.09640.15780.77930.418-0.3707-0.32670.3161-0.0607-0.07990.10880.01450.2831193.2977183.2445561.0652
62.7135-0.22630.30436.3057-1.41524.93680.5779-0.84120.3445-0.24680.05031.2824-0.1634-0.3136-0.48570.3013-0.0579-0.15770.9652-0.57191.0741267.0212222.591592.4005
76.72484.59372.32775.1103-0.43592.88630.0231-0.18550.21830.275-0.44750.1811-0.37460.7170.23750.3756-0.2213-0.06011.0158-0.24981.0308270.5029223.7532582.1274
89.2148-0.22562.64495.5092-3.69781.99990.5239-2.1102-1.87580.30760.55920.88360.6514-1.5813-0.940.5823-0.30550.12231.4523-0.03870.9227276.8099214.8151577.6721
97.6483.01114.02153.98471.2076.5642-0.4175-0.90570.9802-0.08080.10970.2651-0.8313-0.2130.59140.2221-0.14040.01910.8891-0.49120.8157272.6078225.9974590.9327
100.45920.112-0.58247.0902-0.2643.1989-0.1868-0.12720.0864-0.26140.3966-0.06150.0316-0.17680.83630.1836-0.0771-0.0280.4781-0.45120.8408257.5328222.7929581.0439
110.1874-0.6228-0.52354.94644.70994.532-0.56620.45940.573-1.14980.9968-0.2836-0.96710.0154-0.36970.5397-0.0405-0.00070.8136-0.02190.7289259.6979227.9183572.2472
122.4803-2.09420.33851.8374-0.02411.03840.27240.53931.1539-0.19410.186-0.1969-0.07420.0938-0.06030.28390.16990.03821.0970.03620.6053264.0761216.5985573.2057
132.8668-1.06744.00722.4033-2.32635.94340.63651.8275-2.0762-0.4975-0.1459-0.13270.93060.2207-0.54920.44070.1042-0.05721.0442-0.65291.2096270.5066204.9286579.4915
146.74174.67513.78795.9951-1.6798.84980.6198-0.1586-0.7289-0.2440.16390.84150.6813-1.2355-0.68530.3559-0.1297-0.03420.8059-0.08541.2305278.0447210.0165593.4944
153.68080.53613.47442.81411.64665.3146-0.3085-0.89330.6363-0.1645-0.1270.6562-0.7836-0.72990.46410.3024-0.00980.2290.3416-0.06130.3589207.9489212.6684571.1564
160.6651-1.30910.01643.86-1.59251.87580.1109-0.1208-0.41752.2955-0.00230.44820.4428-0.1422-0.04751.0357-0.14910.03150.7035-0.06740.5157229.4309170.5623595.2656
174.48440.37530.30075.59391.82283.7278-0.0701-0.058-0.43811.24670.4902-0.38080.23250.5469-0.33480.84660.0657-0.14040.4818-0.09510.3524233.3295167.2382589.0704
182.8501-1.51740.32072.90120.33590.2033-0.1198-0.87460.18891.12560.2509-0.70.22890.1484-0.06050.71970.0095-0.17180.5715-0.05950.2455235.958175.0878585.476
193.50110.22960.8012.14750.19020.7016-0.1634-1.31910.6750.2354-0.60520.8777-0.2028-0.10720.63140.2552-0.13940.08011.0505-0.39110.7662288.5635228.6863605.6009
204.32070.0195-1.32252.57090.03270.4060.9451-2.4236-1.02960.6034-0.37420.27990.5306-0.019-0.4680.5283-0.3566-0.00031.4478-0.00040.8513288.6735218.5605607.9869
215.1490.0082-2.5325.37462.98635.81550.4282-3.0240.5471-0.0831-0.4538-0.10540.09090.14130.07330.7279-0.2950.04581.6689-0.33920.5264285.6024223.8409613.2476
221.15490.28921.1490.89870.67571.29910.4447-1.1608-0.37830.5363-0.48140.00340.4278-1.21260.04740.532-0.20520.0850.9479-0.08240.3465300.6995228.2179610.5204
238.5431.66657.7568.43192.06157.0793-0.09160.7794-1.6756-0.52040.3945-3.3183-0.0121.984-0.00030.6374-0.14740.28280.4451-0.04331.5394340.3105231.5569603.5729
245.9422-2.05040.15534.6331.54942.04640.19980.23070.3589-0.16330.0209-0.8045-0.4618-0.414-0.18650.39310.14320.09960.0346-0.06750.4239320.6474234.8231606.8908
257.4104-0.5486-0.99551.77063.23265.87760.1902-0.53740.7761-0.46430.2166-0.8323-1.04590.9127-0.41560.4537-0.05650.13730.29650.01990.8682328.6977242.2564604.5167
263.2617-0.86781.8251.11190.51853.34850.9516-0.3399-1.05780.01020.36810.27110.9327-0.0815-0.05510.3264-0.1187-0.34330.3479-0.05540.7965305.863209.8574592.1773
276.7835-4.5431-4.92856.252-0.68718.5411.36590.6507-3.49270.2713-0.64160.77650.9356-1.5264-0.84940.5472-0.1082-0.15110.90760.21371.1227288.4805202.5452596.3608
281.69630.39031.09993.17493.16564.33640.3688-0.0616-0.2161-0.5541-0.23170.4745-0.0652-0.52820.06480.1253-0.1494-0.12130.32-0.29710.3417297.3363219.4331593.6838
291.5146-0.6048-0.38071.70240.44450.53240.3849-0.2684-0.75650.0246-0.22970.1190.3617-0.1887-0.20350.3541-0.1348-0.00220.28050.01280.7923294.3396211.5402586.4319
304.37960.44952.02564.17460.01414.84380.5897-0.5993-0.81550.07940.18810.35211.2004-1.2294-0.21830.1885-0.2305-0.20460.5918-0.04920.521298.1661214.2756594.2927
311.91320.24610.15261.308-0.93552.7633-0.2173-0.42230.05110.14530.1869-0.1758-0.2859-0.02440.02730.12190.0652-0.12870.3089-0.31580.5564325.7742225.3611603.5974
326.8355-0.5023.37994.0784-0.10645.87570.0362-0.8124-1.39630.97020.6022-0.04440.4794-0.4119-0.59960.2990.0387-0.05470.2637-0.04410.5731328.4453219.041607.0896
335.5042-1.23083.16134.8984-2.33916.87650.7969-0.54090.10760.06840.29650.8033-0.2065-0.3701-0.96250.2786-0.00720.17340.1515-0.1180.7405320.0654222.9753601.365
344.2306-1.271-2.87334.96562.20262.3542-0.1519-1.086-0.47651.21690.6528-0.38040.55990.9674-0.53760.53970.2883-0.13410.3177-0.01710.7642333.8668221.1168611.9672
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 20 through 82 )
2X-RAY DIFFRACTION2chain 'A' and (resid 83 through 166 )
3X-RAY DIFFRACTION3chain 'A' and (resid 167 through 334 )
4X-RAY DIFFRACTION4chain 'A' and (resid 335 through 514 )
5X-RAY DIFFRACTION5chain 'A' and (resid 515 through 674 )
6X-RAY DIFFRACTION6chain 'B' and (resid 27 through 47 )
7X-RAY DIFFRACTION7chain 'B' and (resid 48 through 52 )
8X-RAY DIFFRACTION8chain 'B' and (resid 53 through 57 )
9X-RAY DIFFRACTION9chain 'B' and (resid 58 through 77 )
10X-RAY DIFFRACTION10chain 'B' and (resid 78 through 102 )
11X-RAY DIFFRACTION11chain 'B' and (resid 103 through 111 )
12X-RAY DIFFRACTION12chain 'B' and (resid 112 through 117 )
13X-RAY DIFFRACTION13chain 'B' and (resid 118 through 127 )
14X-RAY DIFFRACTION14chain 'B' and (resid 128 through 135 )
15X-RAY DIFFRACTION15chain 'C' and (resid 43 through 79 )
16X-RAY DIFFRACTION16chain 'C' and (resid 80 through 109 )
17X-RAY DIFFRACTION17chain 'C' and (resid 110 through 183 )
18X-RAY DIFFRACTION18chain 'C' and (resid 184 through 219 )
19X-RAY DIFFRACTION19chain 'H' and (resid 1 through 39 )
20X-RAY DIFFRACTION20chain 'H' and (resid 40 through 59 )
21X-RAY DIFFRACTION21chain 'H' and (resid 60 through 83 )
22X-RAY DIFFRACTION22chain 'H' and (resid 84 through 125 )
23X-RAY DIFFRACTION23chain 'H' and (resid 126 through 136 )
24X-RAY DIFFRACTION24chain 'H' and (resid 137 through 182 )
25X-RAY DIFFRACTION25chain 'H' and (resid 183 through 213 )
26X-RAY DIFFRACTION26chain 'L' and (resid 1 through 22 )
27X-RAY DIFFRACTION27chain 'L' and (resid 23 through 37 )
28X-RAY DIFFRACTION28chain 'L' and (resid 38 through 53 )
29X-RAY DIFFRACTION29chain 'L' and (resid 54 through 80 )
30X-RAY DIFFRACTION30chain 'L' and (resid 81 through 105 )
31X-RAY DIFFRACTION31chain 'L' and (resid 106 through 134 )
32X-RAY DIFFRACTION32chain 'L' and (resid 135 through 160 )
33X-RAY DIFFRACTION33chain 'L' and (resid 161 through 178 )
34X-RAY DIFFRACTION34chain 'L' and (resid 179 through 217 )

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • 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

Read more