[English] 日本語
Yorodumi
- PDB-5i8r: aSMase with zinc -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5i8r
TitleaSMase with zinc
ComponentsSphingomyelin phosphodiesterase
KeywordsHYDROLASE / acid sphingomyelinase / olipudase alfa / zinc
Function / homology
Function and homology information


acid sphingomyelin phosphodiesterase activity / sphingomyelin metabolic process / sphingomyelin catabolic process / sphingomyelin phosphodiesterase / lamellar body / sphingomyelin phosphodiesterase activity / phospholipase C / phosphatidylcholine phospholipase C activity / endolysosome / termination of signal transduction ...acid sphingomyelin phosphodiesterase activity / sphingomyelin metabolic process / sphingomyelin catabolic process / sphingomyelin phosphodiesterase / lamellar body / sphingomyelin phosphodiesterase activity / phospholipase C / phosphatidylcholine phospholipase C activity / endolysosome / termination of signal transduction / glycosphingolipid catabolic process / ceramide biosynthetic process / Glycosphingolipid catabolism / plasma membrane repair / response to type I interferon / hydrolase activity, acting on glycosyl bonds / response to ionizing radiation / positive regulation of endocytosis / response to tumor necrosis factor / positive regulation of protein dephosphorylation / cholesterol metabolic process / cellular response to calcium ion / lipid droplet / lysosomal lumen / response to interleukin-1 / negative regulation of MAP kinase activity / response to cocaine / response to virus / wound healing / cellular response to UV / nervous system development / positive regulation of viral entry into host cell / lysosome / endosome / response to xenobiotic stimulus / symbiont entry into host cell / positive regulation of apoptotic process / signal transduction / extracellular space / extracellular exosome / zinc ion binding / plasma membrane
Similarity search - Function
Sphingomyelin phosphodiesterase / Acid sphingomyelinase/endopolyphosphatase, metallophosphatase domain / Sphingomyelin phosphodiesterase, C-terminal domain / Acid sphingomyelin phosphodiesterase C-terminal region / Saposin (B) Domains / Saposin B type domain / Saposin-like / Saposin B type domain profile. / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like
Similarity search - Domain/homology
beta-D-mannopyranose / alpha-D-mannopyranose / Sphingomyelin phosphodiesterase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.646 Å
AuthorsZhou, Y.F. / Wei, R.R.
CitationJournal: Nat Commun / Year: 2016
Title: Human acid sphingomyelinase structures provide insight to molecular basis of Niemann-Pick disease.
Authors: Zhou, Y.F. / Metcalf, M.C. / Garman, S.C. / Edmunds, T. / Qiu, H. / Wei, R.R.
History
DepositionFeb 19, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2016Group: Database references
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_struct_conn_angle / pdbx_struct_oper_list / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_seq_id_1 / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 27, 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
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: Sphingomyelin phosphodiesterase
B: Sphingomyelin phosphodiesterase
C: Sphingomyelin phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)201,86031
Polymers195,3433
Non-polymers6,51728
Water0
1
A: Sphingomyelin phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,56012
Polymers65,1141
Non-polymers2,44611
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Sphingomyelin phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,74511
Polymers65,1141
Non-polymers2,63110
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Sphingomyelin phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,5548
Polymers65,1141
Non-polymers1,4407
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)191.020, 230.870, 252.320
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

-
Components

-
Protein / Non-polymers , 2 types, 9 molecules ABC

#1: Protein Sphingomyelin phosphodiesterase / / Acid sphingomyelinase / aSMase


Mass: 65114.270 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SMPD1, ASM / Production host: Cricetulus griseus (Chinese hamster) / Strain (production host): CHO
References: UniProt: P17405, sphingomyelin phosphodiesterase
#7: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn

-
Sugars , 5 types, 22 molecules

#2: 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.: 5
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
#3: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#4: 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.: 13
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
#5: Sugar ChemComp-BMA / beta-D-mannopyranose / beta-D-mannose / D-mannose / mannose / Mannose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DManpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-mannopyranoseCOMMON NAMEGMML 1.0
b-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0
#6: Sugar ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose / Mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 6.4 Å3/Da / Density % sol: 81 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: 1.5 M ammonium sulfate, 0.1 M sodium acetate pH 5.0-5.5, 12% glycerol
PH range: 5.0-5.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 1.282 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Sep 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.282 Å / Relative weight: 1
ReflectionResolution: 3.646→45 Å / Num. obs: 118927 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 6.9 % / Biso Wilson estimate: 187.51 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.229 / Net I/σ(I): 7.44
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
3.65-3.745.3490.34186.3
3.74-3.844.8050.5199.9
3.84-3.954.0250.63199.9
3.95-4.082.7880.961100
4.08-4.212.091.31100
4.21-4.361.4341.9199.9
4.36-4.520.9992.721100
4.52-4.710.7293.63199.9
4.71-4.920.6014.261100
4.92-5.160.5054.961100
5.16-5.440.4525.38199.9
5.44-5.770.45.891100
5.77-6.160.3187.291100
6.16-6.660.239.411100
6.66-7.290.1314.971100
7.29-8.150.07921.621100
8.15-9.410.04832.91100
9.41-11.530.03839.51100
11.53-16.310.03642.561100
16.31-450.03245.78194.6

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
PHENIX(dev_2229: ???)refinement
HKL-2000data collection
XDSdata reduction
XSCALEdata scaling
PHASER2.5.7phasing
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5I81

5i81


Resolution: 3.646→44.128 Å / SU ML: 0.7 / Cross valid method: FREE R-VALUE / σ(F): 1.87 / Phase error: 34.14 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2535 3840 3.24 %
Rwork0.2482 --
obs0.2484 118574 98.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.646→44.128 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12483 0 400 0 12883
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01313368
X-RAY DIFFRACTIONf_angle_d0.93118295
X-RAY DIFFRACTIONf_dihedral_angle_d12.6637825
X-RAY DIFFRACTIONf_chiral_restr0.0512006
X-RAY DIFFRACTIONf_plane_restr0.0072334
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.6461-3.69220.4938980.532903X-RAY DIFFRACTION67
3.6922-3.74080.47721460.47264298X-RAY DIFFRACTION100
3.7408-3.7920.46681390.48974268X-RAY DIFFRACTION100
3.792-3.84610.41421420.43754347X-RAY DIFFRACTION100
3.8461-3.90350.42191420.43674257X-RAY DIFFRACTION100
3.9035-3.96450.42191450.4224303X-RAY DIFFRACTION100
3.9645-4.02940.42131440.41164269X-RAY DIFFRACTION100
4.0294-4.09890.4371430.39334307X-RAY DIFFRACTION100
4.0989-4.17330.33471450.37694356X-RAY DIFFRACTION100
4.1733-4.25360.32991390.34164267X-RAY DIFFRACTION100
4.2536-4.34030.32991450.31974314X-RAY DIFFRACTION100
4.3403-4.43460.3111430.30114297X-RAY DIFFRACTION100
4.4346-4.53770.31311410.28194310X-RAY DIFFRACTION100
4.5377-4.6510.30281410.26624311X-RAY DIFFRACTION100
4.651-4.77660.24491410.25754308X-RAY DIFFRACTION100
4.7766-4.9170.23771440.24134277X-RAY DIFFRACTION100
4.917-5.07550.25871450.23974296X-RAY DIFFRACTION100
5.0755-5.25660.27181470.23454313X-RAY DIFFRACTION100
5.2566-5.46670.28931460.24684296X-RAY DIFFRACTION100
5.4667-5.7150.2671450.24794276X-RAY DIFFRACTION100
5.715-6.01560.2541420.25024309X-RAY DIFFRACTION100
6.0156-6.39150.2441460.23934309X-RAY DIFFRACTION100
6.3915-6.88330.21261480.22454317X-RAY DIFFRACTION100
6.8833-7.57280.22681420.20394327X-RAY DIFFRACTION100
7.5728-8.66140.18351450.18714297X-RAY DIFFRACTION100
8.6614-10.88530.16581520.16484317X-RAY DIFFRACTION100
10.8853-44.13110.23561440.23284285X-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)
10.3095-0.20060.42061.3048-1.13021.55120.8130.0580.4916-1.13871.02340.15490.67230.02970.33451.6004-0.30480.47672.1631-1.03922.9176230.583322.463852.7848
2-0.0109-0.13980.29170.0628-0.1669-0.0710.14970.12270.18260.2995-0.0415-0.9628-0.86660.9205-0.00071.8839-0.38410.25431.9926-0.45753.4297226.300343.041648.7335
31.1260.30730.34270.38380.14910.98880.1135-0.1381-0.783-0.30280.24210.1410.12190.06270.00021.46540.03720.11941.5725-0.16882.3971197.437619.590343.3404
40.4736-0.01570.1830.4207-0.20880.19610.12010.55280.9364-0.46160.2481-0.7008-0.01330.6386-01.8787-0.09930.48071.956-0.36172.4883209.463133.614534.4418
50.55970.2397-0.38530.4390.06910.54070.1007-0.20460.58240.01310.30020.4488-0.37-0.053901.6898-0.06880.38181.6534-0.31022.2042197.054239.478345.0535
60.7127-0.15130.32940.5334-0.25871.04680.0838-0.18010.13580.13840.117-0.0165-0.2056-0.2255-01.7108-0.00470.38721.8185-0.1322.6305188.62133.105556.2755
70.11320.1446-0.2610.2353-0.32650.71.7361.4202-0.7158-0.44311.05851.6609-1.1334-0.92150.81983.19820.1709-0.24644.7869-2.11782.4392135.48666.25255.1762
80.9641-0.1204-0.07590.05870.04970.02780.12811.00891.663-0.4216-0.3549-0.67860.26110.2857-0.00623.84890.8747-0.03374.2024-1.54031.8547151.097610.2433-8.9789
90.1189-0.17980.20830.21050.39960.31791.08130.00790.1282-0.0132-1.03341.6868-0.7688-1.1918-1.26873.17560.15980.37782.6204-0.94961.2863145.691137.19716.5897
100.16560.32980.2660.16970.15280.017-0.20161.6907-0.946-1.40360.32261.29570.6816-0.517104.07030.290.09173.3788-0.96672.1944146.221433.0951-3.5047
110.06360.25460.49710.26520.63640.57110.33190.428-1.0682-0.2548-0.56420.1009-0.70910.143-03.03130.32660.46893.1676-0.74951.8408161.493734.49264.6046
12-0.01680.1581-0.28370.1493-0.24070.13710.21590.4432-0.1438-0.3635-0.2414-0.169-0.1831-0.065902.7670.06720.57622.9304-0.65781.9841165.881233.683419.3481
130.1049-0.22450.0362-0.0314-0.2669-0.06040.10330.05211.1914-0.2307-0.1513-0.856-0.12111.2068-0.00431.87820.3323-0.18131.9692-0.74492.5586148.969284.730771.8973
14-0.06410.05740.0308-0.04630.01340.08340.4218-0.12320.103-0.4134-0.00370.2649-0.3528-0.1385-0.00012.08530.6885-0.34462.4221-0.63512.6441138.275782.915553.5119
150.162-0.0717-0.09780.33030.04630.1082-0.1877-0.37051.06470.2913-0.1959-0.6652-0.23590.1003-0.00021.85590.30870.15521.7938-0.20471.9049172.151566.636853.6974
160.1911-0.1091-0.23810.39920.08720.21110.3092-0.15121.3937-1.0521-0.77390.4442-1.1742-0.3999-02.47040.3231-0.06952.0271-0.20922.7563160.35980.562244.2827
170.1971-0.2401-0.19990.15740.0670.0464-0.00570.42930.0267-0.1493-0.57020.21520.4139-0.410402.05120.261-0.02412.011-0.46432.1989157.097463.890340.8445
180.3849-0.5575-0.22410.3207-0.02340.3979-0.16790.0306-0.7413-0.4382-0.2348-0.46030.2223-0.2883-02.10740.20980.28912.0232-0.47451.8134160.353650.581447.9422
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 84 through 148 )
2X-RAY DIFFRACTION2chain 'A' and (resid 149 through 181 )
3X-RAY DIFFRACTION3chain 'A' and (resid 182 through 324 )
4X-RAY DIFFRACTION4chain 'A' and (resid 325 through 416 )
5X-RAY DIFFRACTION5chain 'A' and (resid 417 through 510 )
6X-RAY DIFFRACTION6chain 'A' and (resid 511 through 611 )
7X-RAY DIFFRACTION7chain 'C' and (resid 84 through 148 )
8X-RAY DIFFRACTION8chain 'C' and (resid 149 through 181 )
9X-RAY DIFFRACTION9chain 'C' and (resid 182 through 324 )
10X-RAY DIFFRACTION10chain 'C' and (resid 325 through 416 )
11X-RAY DIFFRACTION11chain 'C' and (resid 417 through 510 )
12X-RAY DIFFRACTION12chain 'C' and (resid 511 through 611 )
13X-RAY DIFFRACTION13chain 'B' and (resid 84 through 148 )
14X-RAY DIFFRACTION14chain 'B' and (resid 149 through 181 )
15X-RAY DIFFRACTION15chain 'B' and (resid 182 through 324 )
16X-RAY DIFFRACTION16chain 'B' and (resid 325 through 416 )
17X-RAY DIFFRACTION17chain 'B' and (resid 417 through 510 )
18X-RAY DIFFRACTION18chain 'B' and (resid 511 through 611 )

+
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