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- PDB-3b5h: Crystal structure of the extracellular portion of HAb18G/CD147 -

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Basic information

Entry
Database: PDB / ID: 3b5h
TitleCrystal structure of the extracellular portion of HAb18G/CD147
ComponentsCervical EMMPRIN
KeywordsCELL INVASION / Ig-like domain
Function / homology
Function and homology information


Defective SLC16A1 causes symptomatic deficiency in lactate transport (SDLT) / Proton-coupled monocarboxylate transport / positive regulation of matrix metallopeptidase secretion / acrosomal membrane / response to mercury ion / endothelial tube morphogenesis / neural retina development / photoreceptor cell maintenance / Basigin interactions / Aspirin ADME ...Defective SLC16A1 causes symptomatic deficiency in lactate transport (SDLT) / Proton-coupled monocarboxylate transport / positive regulation of matrix metallopeptidase secretion / acrosomal membrane / response to mercury ion / endothelial tube morphogenesis / neural retina development / photoreceptor cell maintenance / Basigin interactions / Aspirin ADME / odontogenesis of dentin-containing tooth / D-mannose binding / decidualization / positive regulation of vascular endothelial growth factor production / photoreceptor outer segment / lateral plasma membrane / Integrin cell surface interactions / response to cAMP / neutrophil chemotaxis / embryo implantation / Degradation of the extracellular matrix / photoreceptor inner segment / positive regulation of endothelial cell migration / protein localization to plasma membrane / sarcolemma / response to peptide hormone / positive regulation of interleukin-6 production / melanosome / signaling receptor activity / virus receptor activity / basolateral plasma membrane / angiogenesis / positive regulation of viral entry into host cell / cell surface receptor signaling pathway / endosome / cadherin binding / Golgi membrane / intracellular membrane-bounded organelle / focal adhesion / endoplasmic reticulum membrane / mitochondrion / extracellular exosome / membrane / plasma membrane
Similarity search - Function
Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold ...Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / Basigin / Basigin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å
AuthorsYu, X.-L. / Chen, Z.-N.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Crystal structure of HAb18G/CD147: implications for immunoglobulin superfamily homophilic adhesion.
Authors: Yu, X.L. / Hu, T. / Du, J.M. / Ding, J.P. / Yang, X.M. / Zhang, J. / Yang, B. / Shen, X. / Zhang, Z. / Zhong, W.D. / Wen, N. / Jiang, H. / Zhu, P. / Chen, Z.N.
History
DepositionOct 26, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 6, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cervical EMMPRIN
B: Cervical EMMPRIN
C: Cervical EMMPRIN
D: Cervical EMMPRIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,6295
Polymers80,5704
Non-polymers591
Water54030
1
A: Cervical EMMPRIN


Theoretical massNumber of molelcules
Total (without water)20,1421
Polymers20,1421
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cervical EMMPRIN


Theoretical massNumber of molelcules
Total (without water)20,1421
Polymers20,1421
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Cervical EMMPRIN


Theoretical massNumber of molelcules
Total (without water)20,1421
Polymers20,1421
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Cervical EMMPRIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,2012
Polymers20,1421
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)126.481, 126.481, 169.926
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein
Cervical EMMPRIN / HAb18G/CD147


Mass: 20142.447 Da / Num. of mol.: 4 / Fragment: Extracellular portion, UNP residues 22-205
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BSG / Plasmid: pET21a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): OrigamiB(DE3) / References: UniProt: Q54A51, UniProt: P35613*PLUS
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 4.22 Å3/Da / Density % sol: 70.84 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.5M ammonium sulfate, 0.1M triSodium Citrate dihydrate pH 5.60, 1.0M Lithium Sulfate monohydrate, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONPhoton Factory AR-NW12A11
SYNCHROTRONPhoton Factory AR-NW12A20.9792
Detector
TypeIDDetectorDate
ADSC QUANTUM 2101CCDJun 29, 2007
ADSC QUANTUM 2102CCDJun 29, 2007
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.97921
ReflectionRedundancy: 28.5 % / Av σ(I) over netI: 14.7 / Number: 715768 / Rmerge(I) obs: 0.114 / Χ2: 1.35 / D res high: 3.1 Å / D res low: 50 Å / Num. obs: 25099 / % possible obs: 99.7
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
6.67509710.0832.57623.9
5.36.6710010.0912.36827.6
4.635.310010.0821.79428.5
4.214.6310010.0851.64728.9
3.914.2110010.1091.39129.1
3.683.9110010.1671.1229.3
3.493.6810010.2120.90429.5
3.343.4910010.3230.81729.5
3.213.3410010.4340.59329.7
3.13.2110010.6970.53929.6
ReflectionResolution: 2.8→50 Å / Num. obs: 34141 / % possible obs: 99.4 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.106 / Net I/σ(I): 11.7
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.586 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3data extraction
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.8→39.6 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.876 / SU B: 31.409 / SU ML: 0.289 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.514 / ESU R Free: 0.348 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.294 1731 5.1 %RANDOM
Rwork0.243 ---
obs0.245 34141 98.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.63 Å2
Baniso -1Baniso -2Baniso -3
1-0.43 Å20 Å20 Å2
2--0.43 Å20 Å2
3----0.85 Å2
Refinement stepCycle: LAST / Resolution: 2.8→39.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5527 0 4 30 5561
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0225646
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.461.9547653
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.785717
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.68725.285246
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.05515973
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.81526
X-RAY DIFFRACTIONr_chiral_restr0.1070.2852
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024246
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2460.22089
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3080.23599
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2050.2179
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2330.284
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1710.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3821.53662
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.66725769
X-RAY DIFFRACTIONr_scbond_it1.01132242
X-RAY DIFFRACTIONr_scangle_it1.6764.51884
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellHighest resolution: 2.8 Å / Num. reflection Rwork: 2160 / Total num. of bins used: 20
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)
17.73610.0556-1.222241.2091-35.888155.117-1.58150.6403-0.4295-0.56070.6345-2.26990.5487-0.24640.947-0.3722-0.03080.1307-0.2618-0.2507-0.278815.0312-53.3079-25.1799
28.3139-0.0402-3.893210.3893.70712.5690.01870.3221-0.01910.3977-0.066-1.1407-0.15950.85630.0473-0.5007-0.09930.0643-0.0373-0.0858-0.422615.1454-56.5684-29.4734
310.1059-6.2442-3.224511.41174.41488.52910.0136-0.1343-0.5405-0.2957-0.0991.32050.5468-0.36350.0854-0.1943-0.09240.0607-0.178-0.0703-0.48377.6001-62.0017-33.6104
45.90560.9696-1.53814.74340.33458.91360.42750.30410.4277-0.5697-0.72920.7254-0.24820.1040.3017-0.3243-0.0721-0.0196-0.1789-0.1202-0.48276.7031-54.1216-31.3689
50.7394-1.84581.3644.6073-3.40472.51610.90730.8527-0.8782-0.4453-1.01210.43271.0622-0.81010.1049-0.1011-0.13210.07420.0631-0.08710.1539-5.111-38.7442-33.154
619.6846-3.03494.43493.3726-1.23785.35180.20921.1869-0.4666-0.3122-0.24860.14790.8328-0.87810.0393-0.2216-0.11890.11460.1496-0.1313-0.0437-16.217-33.7836-31.2143
723.3685-8.677112.98919.6879-16.404937.64760.36331.9908-0.5227-0.29150.49360.7532-2.32080.0316-0.8569-0.4219-0.02750.27540.3786-0.1328-0.0097-12.0091-23.1404-34.3849
814.1859-2.0935-1.93244.29570.30460.6813-0.01461.05420.1789-0.4775-0.08710.0831-0.2025-0.53990.1017-0.2599-0.08410.02150.2029-0.0684-0.2076-17.0964-26.1949-32.4761
916.46134.74634.295116.38247.511715.2430.26551.55390.6515-0.56310.1946-0.3403-0.670.4518-0.460.2215-0.02560.1097-0.32130.2243-0.22143.5585-33.6194-7.7544
101.86371.06642.34469.2164-10.284818.65651.03840.72224.30030.6469-1.9877-3.9369-1.43162.06970.94930.1582-0.4264-0.00530.3495-0.07121.016518.8223-32.45531.5755
1115.98685.7534-2.49643.96082.06588.46620.5653-0.5002-0.211-0.12720.1015-0.42040.00420.3193-0.66690.1257-0.06470.0368-0.32490.0734-0.50665.7969-43.13732.6432
1238.6016-4.03373.19149.5567-0.57558.55290.10020.4649-0.2939-0.76040.21410.3858-0.2931-0.2213-0.31430.0132-0.09170.0656-0.28940.0373-0.53263.1902-41.1377-4.8703
1318.17360.11682.08673.66781.1455.4807-0.0726-1.05131.0890.58520.0967-0.2736-0.6331-0.4509-0.02410.141-0.02320-0.12890.0124-0.34312.2364-34.45532.5143
1410.35230.3387-5.88066.84090.227911.8750.53360.1542-0.41860.3182-0.5779-0.7651-0.68841.04380.0443-0.05760.1329-0.2261-0.35130.0290.0793-21.5915-34.831713.9244
1510.77960.1882-4.05358.70640.167413.01880.820.58910.0398-0.4037-0.40620.5057-0.3684-0.4798-0.4138-0.02640.14-0.0797-0.58070.017-0.1006-30.611-30.133514.0529
1619.9398.095-17.933514.9393-13.995627.72350.36721.2998-0.6518-0.74650.10320.79550.1460.0309-0.4704-0.15770.2601-0.2803-0.4884-0.0739-0.0577-26.8569-37.138710.1456
1717.41924.31340.28058.86813.801510.86990.28770.51270.58950.41-0.17860.2538-0.35640.2415-0.1091-0.18380.0170.0056-0.1913-0.0522-0.572810.1751-53.5397-16.2847
1817.43052.8168-6.14547.36670.438712.0964-0.01550.1369-0.6609-0.08370.25950.58660.3075-0.0028-0.244-0.192-0.0046-0.0312-0.34120.025-0.43184.75-56.2993-4.9745
1938.77873.9479-5.993812.2174-3.33314.99810.2641-0.16510.85990.29710.1602-0.2867-0.35561.1814-0.4243-0.0649-0.0585-0.0194-0.1174-0.1316-0.696510.0168-49.5828-9.3524
2012.30274.3441-7.52777.76621.561211.4798-0.5025-0.7893-1.1410.46230.1652-0.81891.07521.63520.3373-0.14030.0607-0.02260.0164-0.0727-0.456713.0541-59.0728-8.7425
213.38642.12160.66761.44851.05223.5011-1.3962-1.5753-2.60261.80320.21890.6776-0.88050.76221.17740.1989-0.2552-0.0020.8005-0.00880.162148.2166-56.369-16.102
2213.7346-12.3029-3.046611.16744.675126.45030.00181.21250.10890.6344-0.7699-0.1278-0.02021.10160.76810.0772-0.03580.03890.50820.29420.167459.8234-60.8426-24.671
2311.86213.7993-2.18921.4132-0.30428.33850.3197-0.4716-0.22090.2715-0.61710.0362-0.1877-0.66440.2974-0.1001-0.00450.05440.3172-0.19880.109141.0027-55.8844-23.5904
245.986-0.355-1.5440.76261.78494.2650.207-0.4111-0.00330.2707-0.45230.0798-0.2157-0.01330.24530.0012-0.06990.02770.24110.01780.081349.2619-54.9659-27.193
256.0674-0.22610.36888.7594-2.75787.1732-0.16960.7051-0.1025-0.4826-0.0079-0.2230.3408-0.28570.1776-0.4535-0.00890.2021-0.16380.08050.00675.6443-22.0348-38.844
2620.43443.2664-7.290670.5704-8.306120.4416-0.10610.77893.1448-3.2404-0.4123-1.03740.0042-1.08930.5185-0.2892-0.00810.15590.10290.13730.32017.567-20.4131-48.263
2720.33462.90485.4212.09262.945720.27560.0394-0.75450.81781.05930.0664-0.0767-0.37560.7057-0.1059-0.3942-0.03410.1924-0.37750.1528-0.022610.4266-18.3768-30.587
289.85091.38644.267510.1812-1.719218.2075-0.5361-0.0130.51080.0398-0.20650.6327-0.3956-1.78210.7426-0.46970.0450.1336-0.18810.0560.16321.4866-19.075-34.9501
2915.08623.24734.8297.1637-0.84977.1530.7374-0.02841.6867-2.04880.2591-1.5716-1.46080.0362-0.99650.2541-0.12930.18020.1160.35760.425111.1236-7.5745-8.6714
3022.5639-25.9956-37.835633.170937.615674.5225-0.55931.45671.7336-0.7919-2.5563-1.2059-3.9533-0.29243.11560.5823-0.40320.10790.713-0.11471.295511.2133.20066.8794
315.5730.69350.5763.84761.154912.10240.20170.25920.81240.07650.0833-0.2682-0.07370.4053-0.2851-0.15-0.0843-0.0123-0.13970.13990.207510.3988-12.8461-1.8853
324.2573-0.0818-1.83838.0262.279411.4776-0.1262-0.32880.98510.89510.3637-0.5354-0.04330.9635-0.2376-0.0706-0.0726-0.0814-0.07710.02330.316111.5839-11.39513.8784
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA23 - 322 - 11
2X-RAY DIFFRACTION2AA33 - 4912 - 28
3X-RAY DIFFRACTION3AA50 - 7129 - 50
4X-RAY DIFFRACTION4AA72 - 9851 - 77
5X-RAY DIFFRACTION5AA99 - 11478 - 93
6X-RAY DIFFRACTION6AA115 - 13594 - 114
7X-RAY DIFFRACTION7AA136 - 145115 - 124
8X-RAY DIFFRACTION8AA146 - 203125 - 182
9X-RAY DIFFRACTION9BB23 - 412 - 20
10X-RAY DIFFRACTION10BB42 - 5021 - 29
11X-RAY DIFFRACTION11BB51 - 6430 - 43
12X-RAY DIFFRACTION12BB65 - 8244 - 61
13X-RAY DIFFRACTION13BB83 - 10562 - 84
14X-RAY DIFFRACTION14BB106 - 13685 - 115
15X-RAY DIFFRACTION15BB137 - 189116 - 168
16X-RAY DIFFRACTION16BB190 - 203169 - 182
17X-RAY DIFFRACTION17CC23 - 432 - 22
18X-RAY DIFFRACTION18CC44 - 6423 - 43
19X-RAY DIFFRACTION19CC65 - 8144 - 60
20X-RAY DIFFRACTION20CC82 - 10461 - 83
21X-RAY DIFFRACTION21CC105 - 11684 - 95
22X-RAY DIFFRACTION22CC117 - 12496 - 103
23X-RAY DIFFRACTION23CC125 - 144104 - 123
24X-RAY DIFFRACTION24CC145 - 202124 - 181
25X-RAY DIFFRACTION25DD23 - 632 - 42
26X-RAY DIFFRACTION26DD64 - 7143 - 50
27X-RAY DIFFRACTION27DD72 - 8851 - 67
28X-RAY DIFFRACTION28DD89 - 10468 - 83
29X-RAY DIFFRACTION29DD105 - 11384 - 92
30X-RAY DIFFRACTION30DD114 - 11993 - 98
31X-RAY DIFFRACTION31DD120 - 14599 - 124
32X-RAY DIFFRACTION32DD146 - 201125 - 180

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  • 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

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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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