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- PDB-2x9m: Hendra virus attachment glycoprotein -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 2x9m
TitleHendra virus attachment glycoprotein
ComponentsGLYCOPROTEIN G
KeywordsVIRAL PROTEIN / PARAMYXOVIRUS / VIRAL SURFACE / NIPAH VIRUS / HENIPAVIRUS / VIRUS ENVELOPE / VIRAL ATTACHMENT / HNV / NIV-G / EFNB3 / EFNB2 / EPHRINB2 / EPHRINB3
Function / homology
Function and homology information


exo-alpha-sialidase activity / host cell surface / host cell surface receptor binding / symbiont entry into host cell / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / membrane
Similarity search - Function
Haemagglutinin-neuraminidase / Haemagglutinin/haemagglutinin-neuraminidase, paramyxovirus / Haemagglutinin-neuraminidase / Neuraminidase - #10 / Sialidase superfamily / 6 Propeller / Neuraminidase / Mainly Beta
Similarity search - Domain/homology
Biological speciesHENDRA VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsBowden, T.A. / Crispin, M. / Harvey, D. / Jones, E.Y. / Stuart, D.I.
CitationJournal: J.Virol. / Year: 2010
Title: Dimeric Architecture of the Hendra Virus Attachment Glycoprotein: Evidence for a Conserved Mode of Assembly.
Authors: Bowden, T.A. / Crispin, M. / Harvey, D.J. / Jones, E.Y. / Stuart, D.I.
History
DepositionMar 23, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 21, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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: GLYCOPROTEIN G
B: GLYCOPROTEIN G
C: GLYCOPROTEIN G
D: GLYCOPROTEIN G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)191,03814
Polymers188,8264
Non-polymers2,21210
Water2,108117
1
B: GLYCOPROTEIN G
D: GLYCOPROTEIN G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,5197
Polymers94,4132
Non-polymers1,1065
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2830 Å2
ΔGint5.2 kcal/mol
Surface area35160 Å2
MethodPISA
2
A: GLYCOPROTEIN G
C: GLYCOPROTEIN G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,5197
Polymers94,4132
Non-polymers1,1065
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2890 Å2
ΔGint4.6 kcal/mol
Surface area35190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.883, 84.775, 91.548
Angle α, β, γ (deg.)103.39, 99.63, 108.62
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Ens-ID: 1 / Refine code: 3

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLNGLNLYSLYSAA187 - 1923 - 8
21GLNGLNLYSLYSBB187 - 1923 - 8
31GLNGLNLYSLYSCC187 - 1923 - 8
41GLNGLNLYSLYSDD187 - 1923 - 8
12THRTHRPROPROAA196 - 20812 - 24
22THRTHRPROPROBB196 - 20812 - 24
32THRTHRPROPROCC196 - 20812 - 24
42THRTHRPROPRODD196 - 20812 - 24
13GLYGLYGLYGLYAA214 - 23830 - 54
23GLYGLYGLYGLYBB214 - 23830 - 54
33GLYGLYGLYGLYCC214 - 23830 - 54
43GLYGLYGLYGLYDD214 - 23830 - 54
14ALAALATHRTHRAA245 - 28561 - 101
24ALAALATHRTHRBB245 - 28561 - 101
34ALAALATHRTHRCC245 - 28561 - 101
44ALAALATHRTHRDD245 - 28561 - 101
15VALVALSERSERAA300 - 403116 - 219
25VALVALSERSERBB300 - 403116 - 219
35VALVALSERSERCC300 - 403116 - 219
45VALVALSERSERDD300 - 403116 - 219
16SERSERLEULEUAA405 - 420221 - 236
26SERSERLEULEUBB405 - 420221 - 236
36SERSERLEULEUCC405 - 420221 - 236
46SERSERLEULEUDD405 - 420221 - 236
17LEULEULEULEUAA426 - 567242 - 383
27LEULEULEULEUBB426 - 567242 - 383
37LEULEULEULEUCC426 - 567242 - 383
47LEULEULEULEUDD426 - 567242 - 383
18VALVALILEILEAA571 - 580387 - 396
28VALVALILEILEBB571 - 580387 - 396
38VALVALILEILECC571 - 580387 - 396
48VALVALILEILEDD571 - 580387 - 396
19VALVALSERSERAA587 - 602403 - 418
29VALVALSERSERBB587 - 602403 - 418
39VALVALSERSERCC587 - 602403 - 418
49VALVALSERSERDD587 - 602403 - 418

NCS oper:
IDCodeMatrixVector
1given(-0.7904, -0.6126, -0.0008), (-0.6126, 0.7904, 0.0053), (-0.0026, 0.0046, -1)62.3459, -23.8757, 107.3583
2given(-0.9073, -0.4114, -0.0869), (-0.4126, 0.9109, -0.0048), (0.0811, 0.0315, -0.9962)50.0494, 10.14, 103.4933
3given(0.9692, 0.2355, 0.0717), (-0.2365, 0.9716, 0.0071), (-0.068, -0.0238, 0.9974)-5.7316, -37.5107, 0.3894

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Components

#1: Protein
GLYCOPROTEIN G / HEV-G


Mass: 47206.543 Da / Num. of mol.: 4 / Fragment: RECEPTOR-BINDING DOMAIN, RESIDUES 185-604
Source method: isolated from a genetically manipulated source
Details: N-ACETYLGLUCOSAMINE LINKAGES OBSERVED IN STRUCTURE ASN306, ASN378, ASN417, ASN481, AND ASN529
Source: (gene. exp.) HENDRA VIRUS / Description: SYNTHETICALLY OPTIMIZED CDNA (GENEART) / Plasmid: PHLSEC / Cell line (production host): 293T / Organ (production host): EMBRYONIC KIDNEY / Production host: HOMO SAPIENS (human) / References: UniProt: O89343
#2: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 117 / 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: 2.4 Å3/Da / Density % sol: 48 % / Description: NONE
Crystal growpH: 6.5
Details: 30% PEG 8000, 0.2 M AMMONIUM SULPHATE, 0.1 M SODIUM CACODYLATE BUFFER PH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 16, 2009 / Details: MIRRORS
RadiationMonochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 38664 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 3 % / Biso Wilson estimate: 37.8 Å2 / Rmerge(I) obs: 0.17 / Net I/σ(I): 6.1
Reflection shellResolution: 2.9→2.95 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 2.9 / % possible all: 98

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VWD
Resolution: 2.9→44.2 Å / Cor.coef. Fo:Fc: 0.876 / Cor.coef. Fo:Fc free: 0.819 / SU B: 42.258 / SU ML: 0.38 / Cross valid method: THROUGHOUT / ESU R Free: 0.489 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. B VALUES HAVE TLS CONTRIBUTION.
RfactorNum. reflection% reflectionSelection details
Rfree0.27273 1926 5 %RANDOM
Rwork0.23306 ---
obs0.23507 36735 98.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 23.765 Å2
Baniso -1Baniso -2Baniso -3
1-0.97 Å20.11 Å2-0.34 Å2
2---0.25 Å2-0.09 Å2
3----0.81 Å2
Refinement stepCycle: LAST / Resolution: 2.9→44.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13207 0 140 117 13464
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.02213706
X-RAY DIFFRACTIONr_bond_other_d0.0030.029182
X-RAY DIFFRACTIONr_angle_refined_deg1.1241.96818687
X-RAY DIFFRACTIONr_angle_other_deg0.904322407
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.32451667
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.70224.286602
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.165152246
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8291572
X-RAY DIFFRACTIONr_chiral_restr0.0870.22107
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02115115
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022691
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_it0.7051.58348
X-RAY DIFFRACTIONr_mcbond_other0.1311.53344
X-RAY DIFFRACTIONr_mcangle_it1.306213630
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.98635358
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.7014.55057
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 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A2192tight positional0.020.05
2B2192tight positional0.020.05
3C2192tight positional0.020.05
4D2192tight positional0.020.05
1A2801loose positional0.055
2B2801loose positional0.035
3C2801loose positional0.045
4D2801loose positional0.055
1A2192tight thermal0.040.5
2B2192tight thermal0.040.5
3C2192tight thermal0.060.5
4D2192tight thermal0.040.5
1A2801loose thermal0.0310
2B2801loose thermal0.0310
3C2801loose thermal0.0410
4D2801loose thermal0.0310
LS refinement shellResolution: 2.899→2.974 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.364 142 -
Rwork0.301 2541 -
obs--93.75 %
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)
12.61360.04662.56982.09770.34563.3622-0.0795-0.2506-0.20440.36240.22320.2126-0.0844-0.4949-0.14380.14480.03520.06090.23270.03310.04470.521127.138744.3179
21.1527-0.04530.91780.0801-0.36112.1049-0.13850.04360.06170.05170.0289-0.0336-0.2417-0.16830.10950.20050.0492-0.12350.0672-0.02880.148817.626732.68241.4327
31.8431-0.04370.2371.6313-0.01741.7316-0.1661-0.15650.0640.23470.1054-0.26880.0066-0.08450.06070.16120.0402-0.05060.075-0.00110.05919.974127.180742.3214
41.3007-0.33540.62291.2205-0.42061.4064-0.00430.0880.0349-0.1061-0.0135-0.0610.07540.00010.01780.13420.00720.00160.033-0.01220.016512.480229.226524.0805
52.3467-0.79061.2080.38390.01242.12-0.1391-0.5404-0.16590.11060.1090.09370.2076-0.45440.03010.1761-0.00370.05210.16540.03140.04973.443223.816642.1041
62.63772.79321.73184.62851.09071.9405-0.1378-0.34960.36180.31050.11260.4453-0.1927-0.57330.02520.19790.0917-0.00420.2438-0.00220.13712.674333.425944.1082
72.34130.03021.89941.5431.21553.48930.0770.2719-0.0463-0.45440.0941-0.2145-0.41450.425-0.17110.2546-0.08240.07050.15110.02560.06118.05377.961563.4415
81.92020.1382-0.63420.46480.9112.24150.0492-0.0769-0.0707-0.1807-0.09480.0333-0.366-0.11580.04570.25730.0469-0.11350.0434-0.02740.11670.862371.785866.2924
91.40240.31150.13451.01010.43582.1207-0.06260.1394-0.114-0.2607-0.05190.1907-0.0599-0.03010.11450.20350.0307-0.05910.0555-0.01970.06412.194266.252965.4876
100.9157-0.30870.17751.49151.10732.2458-0.0417-0.089-0.12410.2072-0.08360.20650.2544-0.12430.12520.1862-0.0080.00550.03980.02110.06550.146966.211385.5358
111.07780.0788-0.17591.37240.781.6179-0.0138-0.01580.0228-0.08160.09-0.0695-0.12130.2055-0.07620.16170.0088-0.02760.07060.00830.025313.564477.093780.6426
1210.1911-2.01191.85231.4106-0.03021.2020.0849-0.17810.4995-0.51170.0394-0.0366-0.48640.2569-0.12430.4542-0.08770.07110.1782-0.07780.114912.294881.498163.5896
131.8306-0.6390.00630.56050.46022.63980.24430.5910.1153-0.3247-0.1201-0.1885-0.22240.5512-0.12420.2969-0.03050.03850.35890.0820.158130.553735.458362.4739
140.9798-0.10140.4271.18360.26612.2998-0.0116-0.0086-0.04330.00390.0230.14510.0603-0.2139-0.01140.14650.01290.00410.05070.03780.058712.895226.621276.6175
152.6385-0.4067-10.5670.06351.633742.3537-0.64360.0797-0.2660.0497-0.23130.04521.6668-0.44310.87490.5080.1856-0.0680.56550.00950.49587.07938.282679.6619
161.42060.06030.13721.41710.23441.8129-0.0687-0.02630.13670.07380.0739-0.1637-0.20820.2-0.00510.17040.0038-0.03560.06880.01350.054227.954334.362980.2465
1715.5294-11.624615.38368.7914-11.517215.2394-0.273-0.5562-0.31660.20450.60520.3412-0.2622-0.5544-0.33210.72230.0119-0.13240.50160.2590.160617.918446.421762.2929
1810.2096-2.08511.61170.7788-0.26373.59660.25390.31030.3209-0.4485-0.0729-0.1906-0.17140.4896-0.1810.476-0.05940.12160.16090.05290.118532.80535.799863.4348
192.42390.40141.96431.06080.5543.2786-0.0862-0.3569-0.06170.3670.09160.29630.1568-0.6656-0.00540.2033-0.02750.13030.27240.04280.1004-13.922662.265344.0183
200.6591.0555-0.14781.93340.33192.41740.0568-0.0309-0.02070.1528-0.0161-0.1303-0.332-0.0783-0.04070.23510.0591-0.07170.0868-0.05710.1053.479575.641243.1724
210.79610.09450.56981.0898-0.20052.3269-0.05550.05240.03230.02690.0357-0.1018-0.08280.23620.01980.13770.00970.00850.066-0.00880.05038.72169.404929.2684
221.2610.21570.38770.9852-0.04412.151-0.068-0.0640.027-0.03910.07740.1483-0.0498-0.3262-0.00940.13650.0249-0.00670.08850.00020.0597-8.047466.616927.6934
2341.2799-5.24949.04863.7079-1.67312.0766-0.8135-0.907-0.78480.42721.02440.4149-0.2305-0.386-0.21080.3670.14150.06730.5517-0.12620.3234-8.558583.577146.1736
244.76083.70671.30253.68581.55682.98530.139-0.3014-0.01630.5269-0.0260.16820.1178-0.6154-0.11290.26130.12760.12430.33240.10140.0689-12.605765.175144.3909
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A185 - 212
2X-RAY DIFFRACTION2A213 - 239
3X-RAY DIFFRACTION3A240 - 289
4X-RAY DIFFRACTION4A290 - 567
5X-RAY DIFFRACTION5A568 - 580
6X-RAY DIFFRACTION6A581 - 603
7X-RAY DIFFRACTION7B185 - 212
8X-RAY DIFFRACTION8B213 - 239
9X-RAY DIFFRACTION9B240 - 289
10X-RAY DIFFRACTION10B290 - 419
11X-RAY DIFFRACTION11B421 - 580
12X-RAY DIFFRACTION12B581 - 603
13X-RAY DIFFRACTION13C186 - 215
14X-RAY DIFFRACTION14C216 - 419
15X-RAY DIFFRACTION15C420 - 425
16X-RAY DIFFRACTION16C426 - 579
17X-RAY DIFFRACTION17C580 - 586
18X-RAY DIFFRACTION18C587 - 603
19X-RAY DIFFRACTION19D186 - 210
20X-RAY DIFFRACTION20D211 - 244
21X-RAY DIFFRACTION21D245 - 419
22X-RAY DIFFRACTION22D420 - 580
23X-RAY DIFFRACTION23D581 - 586
24X-RAY DIFFRACTION24D587 - 603

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  • 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

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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

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