[English] 日本語
Yorodumi
- PDB-6f5m: Crystal structure of highly glycosylated human leukocyte elastase... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6f5m
TitleCrystal structure of highly glycosylated human leukocyte elastase in complex with a thiazolidinedione inhibitor
ComponentsNeutrophil elastase
KeywordsHYDROLASE / human leukocyte elastase / human neutrophil elastase / parabolic inhibition / glycosylation
Function / homology
Function and homology information


leukocyte elastase / biosynthetic process of antibacterial peptides active against Gram-negative bacteria / neutrophil-mediated killing of fungus / acute inflammatory response to antigenic stimulus / negative regulation of chemotaxis / positive regulation of leukocyte tethering or rolling / response to yeast / leukocyte migration involved in inflammatory response / negative regulation of interleukin-8 production / negative regulation of chemokine production ...leukocyte elastase / biosynthetic process of antibacterial peptides active against Gram-negative bacteria / neutrophil-mediated killing of fungus / acute inflammatory response to antigenic stimulus / negative regulation of chemotaxis / positive regulation of leukocyte tethering or rolling / response to yeast / leukocyte migration involved in inflammatory response / negative regulation of interleukin-8 production / negative regulation of chemokine production / Antimicrobial peptides / pyroptotic inflammatory response / Activation of Matrix Metalloproteinases / neutrophil-mediated killing of gram-negative bacterium / cytokine binding / Collagen degradation / extracellular matrix disassembly / Pyroptosis / phagocytosis / response to UV / phagocytic vesicle / transcription repressor complex / Degradation of the extracellular matrix / secretory granule / Regulation of Complement cascade / positive regulation of interleukin-8 production / positive regulation of smooth muscle cell proliferation / positive regulation of MAP kinase activity / protein catabolic process / negative regulation of inflammatory response / intracellular calcium ion homeostasis / specific granule lumen / transcription corepressor activity / positive regulation of immune response / azurophil granule lumen / heparin binding / peptidase activity / protease binding / collagen-containing extracellular matrix / endopeptidase activity / response to lipopolysaccharide / defense response to bacterium / serine-type endopeptidase activity / Neutrophil degranulation / negative regulation of transcription by RNA polymerase II / cell surface / proteolysis / extracellular space / extracellular exosome / extracellular region / cytosol / cytoplasm
Similarity search - Function
: / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin ...: / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / Chem-CQH / Neutrophil elastase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsHochscherf, J. / Pietsch, M. / Tieu, W. / Kuan, K. / Hautmann, S. / Abell, A. / Guetschow, M. / Niefind, K.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationNI 643/4-1 Germany
Citation
Journal: Acta Crystallogr F Struct Biol Commun / Year: 2018
Title: Crystal structure of highly glycosylated human leukocyte elastase in complex with an S2' site binding inhibitor.
Authors: Hochscherf, J. / Pietsch, M. / Tieu, W. / Kuan, K. / Abell, A.D. / Gutschow, M. / Niefind, K.
#1: Journal: J. Mol. Biol. / Year: 2011
Title: Unexpected active-site flexibility in the structure of human neutrophil elastase in complex with a new dihydropyrimidone inhibitor.
Authors: Hansen, G. / Gielen-Haertwig, H. / Reinemer, P. / Schomburg, D. / Harrenga, A. / Niefind, K.
#2: Journal: Bioorg. Med. Chem. Lett. / Year: 2012
Title: 5-benzylidenerhodanine and 5-benzylidene-2-4-thiazolidinedione based antibacterials.
Authors: Zvarec, O. / Polyak, S.W. / Tieu, W. / Kuan, K. / Dai, H. / Pedersen, D.S. / Morona, R. / Zhang, L. / Booker, G.W. / Abell, A.D.
History
DepositionDec 1, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 8, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 15, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.page_first ..._citation.journal_abbrev / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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_special_symmetry / 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 / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _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 2.1Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Neutrophil elastase
B: Neutrophil elastase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,57615
Polymers46,6382
Non-polymers4,93813
Water79344
1
A: Neutrophil elastase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7368
Polymers23,3191
Non-polymers2,4177
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Neutrophil elastase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8397
Polymers23,3191
Non-polymers2,5206
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)204.557, 204.557, 62.155
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-518-

HOH

21B-517-

HOH

31B-521-

HOH

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Neutrophil elastase / Bone marrow serine protease / Elastase-2 / Human leukocyte elastase / HLE / Medullasin / PMN elastase


Mass: 23318.982 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P08246, leukocyte elastase

-
Sugars , 3 types, 4 molecules

#2: Polysaccharide alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 894.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/4,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3-4/a4-b1_a6-e1_b4-c1_c6-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{}}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#3: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 732.682 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1221m-1a_1-5]/1-1-2-3/a4-b1_a6-d1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#4: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1056.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/4,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3-3-4/a4-b1_a6-f1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE

-
Non-polymers , 4 types, 53 molecules

#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C2H3O2
#7: Chemical ChemComp-CQH / 5-[[4-[[(2~{S})-4-methyl-1-oxidanylidene-1-[(2-propylphenyl)amino]pentan-2-yl]carbamoyl]phenyl]methyl]-2-oxidanylidene-1,3-thiazol-1-ium-4-olate


Mass: 479.591 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H29N3O4S
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.68 Å3/Da / Density % sol: 54.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: HLE from human blood was purchased from SERVA as a lyophilisate in the presence of sodium acetate puffer, pH 5.5. The lyophilisate was disolved in water so that the HLE concentration was 5 ...Details: HLE from human blood was purchased from SERVA as a lyophilisate in the presence of sodium acetate puffer, pH 5.5. The lyophilisate was disolved in water so that the HLE concentration was 5 mg/ml (170 micromolar) and the acetate concentration 250 millimolar. 120 microliter dissolved HNE lysophilisate was mixed with 6 microliter inhibitor solution (10 mM in DMSO). 1 microliter of the resulting HLE/inhibitor mixture was mixed with 0.5 microliter reservoir solution which was composed of 20 % PEG MME 5000, 0.2 M potassium sulphate. Repeated seeding was necessary to get usable crystals. In the final seeding step the reservoir was composed of 20 % PEG MME 5000, 0.2 M sodium sulphate.
PH range: 5-7

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Oct 20, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→45.6 Å / Num. obs: 13722 / % possible obs: 99.94 % / Redundancy: 20.7 % / Biso Wilson estimate: 62.04 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.2407 / Rsym value: 0.2407 / Net I/σ(I): 15.4
Reflection shellResolution: 2.7→2.83 Å / Redundancy: 21.6 % / Mean I/σ(I) obs: 1.2 / Num. unique obs: 1808 / CC1/2: 0.442 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PPG
Resolution: 2.7→45.553 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 26.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2336 1046 7.62 %
Rwork0.1758 --
obs0.1804 13721 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7→45.553 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3272 0 329 44 3645
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023685
X-RAY DIFFRACTIONf_angle_d0.5425047
X-RAY DIFFRACTIONf_dihedral_angle_d11.6432164
X-RAY DIFFRACTIONf_chiral_restr0.044617
X-RAY DIFFRACTIONf_plane_restr0.003627
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.84230.35681290.29791814X-RAY DIFFRACTION100
2.8423-3.02040.30321390.27321807X-RAY DIFFRACTION100
3.0204-3.25350.3021420.23081795X-RAY DIFFRACTION100
3.2535-3.58080.27591630.1871793X-RAY DIFFRACTION100
3.5808-4.09870.22351610.16141788X-RAY DIFFRACTION100
4.0987-5.16280.18351440.13141829X-RAY DIFFRACTION100
5.1628-45.55980.20791680.15861849X-RAY DIFFRACTION100
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)
13.1651.2823-0.132.2605-0.35671.04230.02940.313-0.3775-0.18430.248-0.08860.15290.3853-00.42680.0401-0.01550.54330.01960.509643.379324.92124.8767
20.99630.54140.10551.2539-0.13940.46760.23420.5988-0.78990.1149-0.0525-1.07370.66140.4122-0.00090.5010.04540.00940.6661-0.00370.688950.2717.947424.8139
34.0192-0.33120.04773.2315-0.15321.74390.08060.03880.50550.0067-0.0414-0.2224-0.42470.36190.00010.4196-0.07230.00740.49960.07350.467346.313832.604229.7795
40.36260.57120.41841.02010.971.2832-0.54570.49890.3497-1.00290.43890.1525-1.1674-0.23670.00320.84260.0967-0.09650.68480.11730.662533.348338.224516.5296
54.4070.5892-0.91363.45250.75934.74640.01560.2788-0.1827-0.0346-0.08830.33120.229-0.1200.4715-0.0001-0.07280.50180.03620.440629.655225.148420.3002
61.9512-1.67041.39592.4976-0.59832.4887-0.10410.42410.5141-0.03270.19790.1284-0.22090.1225-0.00010.5188-0.00560.05340.54020.09470.490934.73235.190424.2331
74.195-0.4995-0.20223.5328-0.67980.31650.0189-0.2265-0.03080.69330.1962-0.15660.0868-0.04500.62240.037-0.03170.40480.05980.455633.58159.367847.2871
80.3946-0.2835-0.28151.623-0.75260.84230.2017-0.41360.00190.64380.1194-0.77920.33550.62980.03410.67480.0362-0.12620.52130.08450.615943.03266.739547.9531
92.317-0.2622-0.47022.21850.40691.6967-0.0152-0.1065-0.54210.16680.13170.14670.3267-0.172200.56580.0077-0.02150.50270.04560.569828.65612.866842.2471
100.232-0.05790.19440.9725-0.71320.62670.3176-0.6734-0.3421.3089-0.17510.7608-0.3846-0.46870.00290.8805-0.0190.30230.8190.04950.856616.486611.69254.5081
110.91070.17970.34350.115-0.06140.33880.271-0.46411.1648-0.62570.001-0.2481-0.24380.13020.00020.6921-0.08930.00160.5692-0.07880.851838.130222.63450.8312
121.0473-0.3717-1.33842.2358-0.00751.82-0.3103-0.2157-0.10910.01740.11570.6278-0.4321-1.0385-0.00010.69050.09730.05180.80110.03950.709817.961319.335451.0658
132.6592-0.58441.92671.44080.79942.53560.137-0.52060.25590.86850.10830.2626-0.1678-0.643600.81880.02070.11340.5910.04680.622924.496717.22151.3892
140.0914-0.0135-0.03770.2909-0.02360.17880.0420.4633-0.28230.3171-0.60460.2917-0.0657-1.3605-0.00090.99670.1060.12210.71970.07450.749422.308228.087146.5234
151.99090.1545-1.57280.43130.49462.1466-0.36110.1403-0.36371.15730.24261.48960.3011-0.26830.00040.6194-0.0715-0.02930.6160.07480.750718.51153.758344.4036
161.7966-1.2222-0.68472.78661.60620.9261-0.58772.45721.0528-1.70271.1102-0.5228-1.27610.13770.09531.14390.15330.01821.05180.24610.711537.640532.74244.6071
170.18920.14910.02020.17970.15130.2972-0.50640.4116-2.67040.44310.4139-2.36932.58040.7894-0.00031.40920.4162-0.03651.06740.05561.660959.67819.015433.1715
180.31420.09430.06730.02820.02010.01440.2909-2.0422-1.11691.0818-0.34620.9004-0.8101-0.8512-0.00211.32020.13090.09771.49690.38731.019822.229811.121668.4391
190.05050.1589-0.43340.5005-1.36443.7205-0.2701-0.4183-0.42570.6710.4464-2.33580.11582.04620.39360.53230.1267-0.24290.9653-0.35521.58147.2405-1.730840.1192
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 16 through 62A)
2X-RAY DIFFRACTION2chain 'A' and (resid 62B through 80 )
3X-RAY DIFFRACTION3chain 'A' and (resid 81 through 123 )
4X-RAY DIFFRACTION4chain 'A' and (resid 124 through 140 )
5X-RAY DIFFRACTION5chain 'A' and (resid 141 through 197 )
6X-RAY DIFFRACTION6chain 'A' and (resid 198 through 243 )
7X-RAY DIFFRACTION7chain 'B' and (resid 16 through 62A)
8X-RAY DIFFRACTION8chain 'B' and (resid 62B through 80 )
9X-RAY DIFFRACTION9chain 'B' and (resid 81 through 123 )
10X-RAY DIFFRACTION10chain 'B' and (resid 124 through 140 )
11X-RAY DIFFRACTION11chain 'B' and (resid 141 through 155 )
12X-RAY DIFFRACTION12chain 'B' and (resid 156 through 184 )
13X-RAY DIFFRACTION13chain 'B' and (resid 185 through 215 )
14X-RAY DIFFRACTION14chain 'B' and (resid 216 through 225 )
15X-RAY DIFFRACTION15chain 'B' and (resid 226 through 243 )
16X-RAY DIFFRACTION16chain 'A' and (resid 401 through 405)
17X-RAY DIFFRACTION17chain 'A' and (resid 406 through 409)
18X-RAY DIFFRACTION18chain 'B' and (resid 401 through 406)
19X-RAY DIFFRACTION19chain 'B' and (resid 407 through 410)

+
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://pdbjlc1.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