[English] 日本語
Yorodumi
- PDB-9atu: Bifunctional Inhibition of Neutrophil Elastase by Eap4 from S. aureus -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9atu
TitleBifunctional Inhibition of Neutrophil Elastase by Eap4 from S. aureus
Components
  • Extracellular Adherence Protein
  • Neutrophil elastase
KeywordsPROTEIN BINDING / PROTEASE INHIBITOR / IMMUNE EVASION
Function / homology
Function and homology information


leukocyte elastase / biosynthetic process of antibacterial peptides active against Gram-negative bacteria / neutrophil-mediated killing of fungus / Expression of NOTCH2NL genes / negative regulation of chemotaxis / acute inflammatory response to antigenic stimulus / positive regulation of leukocyte tethering or rolling / response to yeast / leukocyte migration involved in inflammatory response / negative regulation of interleukin-8 production ...leukocyte elastase / biosynthetic process of antibacterial peptides active against Gram-negative bacteria / neutrophil-mediated killing of fungus / Expression of NOTCH2NL genes / negative regulation of chemotaxis / acute inflammatory response to antigenic stimulus / 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 / cytokine binding / neutrophil-mediated killing of gram-negative bacterium / Collagen degradation / extracellular matrix disassembly / Pyroptosis / phagocytosis / response to UV / phagocytic vesicle / Degradation of the extracellular matrix / transcription repressor complex / positive regulation of MAP kinase activity / secretory granule / Regulation of Complement cascade / positive regulation of interleukin-8 production / positive regulation of smooth muscle cell proliferation / protein catabolic process / positive regulation of immune response / negative regulation of inflammatory response / specific granule lumen / intracellular calcium ion homeostasis / transcription corepressor activity / azurophil granule lumen / peptidase activity / heparin binding / protease binding / : / endopeptidase activity / response to lipopolysaccharide / defense response to bacterium / serine-type endopeptidase activity / intracellular membrane-bounded organelle / Neutrophil degranulation / negative regulation of transcription by RNA polymerase II / cell surface / Golgi apparatus / proteolysis / extracellular space / extracellular exosome / extracellular region / cytosol / cytoplasm
Similarity search - Function
MAP domain / MAP domain / MAP repeat profile. / : / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. ...MAP domain / MAP domain / MAP repeat profile. / : / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
Neutrophil elastase / Protein map
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus Mu50 (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsMishra, N.B. / Herdendorf, T.J. / Geisbrecht, B.V.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM140852 United States
CitationJournal: J.Biol.Chem. / Year: 2024
Title: S. aureus Eap is a polyvalent inhibitor of neutrophil serine proteases.
Authors: Mishra, N. / Gido, C.D. / Herdendorf, T.J. / Hammel, M. / Hura, G.L. / Fu, Z.Q. / Geisbrecht, B.V.
History
DepositionFeb 27, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / pdbx_entry_details / pdbx_modification_feature
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Neutrophil elastase
B: Extracellular Adherence Protein
C: Neutrophil elastase
D: Neutrophil elastase
F: Neutrophil elastase
E: Extracellular Adherence Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,34014
Polymers117,9496
Non-polymers5,3918
Water6,089338
1
C: Neutrophil elastase
F: Neutrophil elastase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9414
Polymers46,6382
Non-polymers1,3032
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Neutrophil elastase
F: Neutrophil elastase
E: Extracellular Adherence Protein
hetero molecules

A: Neutrophil elastase
B: Extracellular Adherence Protein
C: Neutrophil elastase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,34014
Polymers117,9496
Non-polymers5,3918
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x+1/2,-y+1,z+1/21
Buried area16230 Å2
ΔGint67 kcal/mol
Surface area45840 Å2
MethodPISA
3
A: Neutrophil elastase
B: Extracellular Adherence Protein
C: Neutrophil elastase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,5817
Polymers58,9743
Non-polymers2,6064
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7520 Å2
ΔGint34 kcal/mol
Surface area23550 Å2
MethodPISA
4
A: Neutrophil elastase
B: Extracellular Adherence Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9594
Polymers35,6552
Non-polymers1,3032
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3870 Å2
ΔGint15 kcal/mol
Surface area15000 Å2
MethodPISA
5
D: Neutrophil elastase
F: Neutrophil elastase
E: Extracellular Adherence Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,7597
Polymers58,9743
Non-polymers2,7854
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7250 Å2
ΔGint25 kcal/mol
Surface area23740 Å2
MethodPISA
6
D: Neutrophil elastase
E: Extracellular Adherence Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9754
Polymers35,6552
Non-polymers1,3192
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3490 Å2
ΔGint9 kcal/mol
Surface area15240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.816, 121.060, 147.628
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 2 types, 6 molecules ACDFBE

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


Mass: 23318.982 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell: Neutrophil / References: UniProt: P08246, leukocyte elastase
#2: Protein Extracellular Adherence Protein / Protein map


Mass: 12336.466 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus Mu50 (bacteria)
Gene: map, SAV1938 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q99QS1

-
Sugars , 3 types, 8 molecules

#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.: 5
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam 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
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#5: 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-ROHGlycam 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
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE

-
Non-polymers , 1 types, 338 molecules

#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 338 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.87 Å3/Da / Density % sol: 57.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M ammonium acetate 0.1 M Tris-HCl (pH 8.0) 17% (w/v) PEG-10K

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 2, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 85130 / % possible obs: 99.7 % / Redundancy: 12.8 % / CC1/2: 0.99 / CC star: 0.997 / Rmerge(I) obs: 0.103 / Rpim(I) all: 0.029 / Rrim(I) all: 0.107 / Χ2: 0.981 / Net I/σ(I): 8.6 / Num. measured all: 1088798
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.05-2.129.81.38783740.60.8660.4421.4590.92999.3
2.12-2.2112.21.06484100.8270.9520.3121.1090.92399.9
2.21-2.3112.80.76484360.920.9790.220.7960.972100
2.31-2.4312.20.51684050.9460.9860.1530.5390.9799.2
2.43-2.58140.45384730.9830.9960.1230.471.059100
2.58-2.7813.90.2284820.9910.9980.060.2281.06999.9
2.78-3.0613.50.13785150.9950.9990.0380.1420.95199.9
3.06-3.5112.40.0984820.9960.9990.0270.0940.97999.1
3.51-4.42140.07286620.9970.9990.020.0750.983100
4.42-5012.90.06788910.9870.9970.020.070.94299.3

-
Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→41.28 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 0.24 / Phase error: 25.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2372 1877 2.35 %
Rwork0.1848 --
obs0.186 79893 93.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.05→41.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8118 0 360 338 8816
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0088622
X-RAY DIFFRACTIONf_angle_d0.8811694
X-RAY DIFFRACTIONf_dihedral_angle_d13.3513217
X-RAY DIFFRACTIONf_chiral_restr0.0591439
X-RAY DIFFRACTIONf_plane_restr0.0081474
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.110.37641100.31854769X-RAY DIFFRACTION75
2.11-2.170.29751270.2645264X-RAY DIFFRACTION83
2.17-2.240.28221350.24175554X-RAY DIFFRACTION88
2.24-2.320.29191430.22235784X-RAY DIFFRACTION91
2.32-2.410.26461410.2075866X-RAY DIFFRACTION92
2.41-2.520.26211390.20676064X-RAY DIFFRACTION95
2.52-2.660.27331500.216169X-RAY DIFFRACTION97
2.66-2.820.27261510.22346266X-RAY DIFFRACTION98
2.82-3.040.27891550.21726330X-RAY DIFFRACTION99
3.04-3.350.2611540.20786378X-RAY DIFFRACTION99
3.35-3.830.22041540.17846357X-RAY DIFFRACTION99
3.83-4.830.18911570.1466529X-RAY DIFFRACTION100
4.83-41.280.22131610.15836686X-RAY DIFFRACTION99
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)
15.26962.7487-0.56285.35310.42023.0927-0.20870.2109-0.27330.03440.2327-0.79580.67890.7325-0.06960.2880.0924-0.05910.2807-0.07630.407317.39542.406743.9447
23.27430.3382-0.11235.05650.34042.8127-0.0680.5183-0.0805-0.418-0.00470.09730.17060.01340.01310.27650.0066-0.04880.339-0.05290.28665.2097.43335.0532
32.25631.37070.33143.91630.46152.4779-0.07760.15920.23650.0548-0.06990.70160.1286-0.22060.09950.19810.0172-0.02030.313-0.05770.425-0.986710.241641.9619
44.01340.89160.88654.11120.47393.32010.1178-0.652-0.01160.8416-0.2434-0.0254-0.030.3302-0.03960.4936-0.0483-0.01170.4732-0.06230.370310.496712.659157.1252
53.6324-1.22641.57768.00681.03162.9893-0.12150.03810.28790.20290.3193-0.37970.040.5195-0.25160.1617-0.07380.01290.30240.02210.296517.655915.574645.9575
64.50482.0690.15442.83120.1111.49310.11510.01740.23190.2754-0.07620.1103-0.01270.0964-0.00150.29350.007-0.0380.2351-0.0420.356510.613216.150448.7967
76.1581-1.2712-0.877.80120.62236.96810.370.3925-0.2507-0.8465-0.5467-0.00520.36310.2820.10980.42650.10130.03950.36120.0150.29111.928635.358619.3593
85.025-5.7019-5.25317.91614.13827.82660.32671.1233-0.0991-3.112-0.1525-0.2357-2.08350.3312-0.61950.89590.04710.10650.60190.020.426915.329218.102624.4262
99.19696.4249-4.91144.9548-3.95015.1909-0.07170.2767-0.7866-0.1417-0.1034-1.029-0.17290.26610.17370.37130.08120.01250.4664-0.04230.35218.036733.227527.1513
108.48794.81781.90726.41350.58793.58950.1948-0.16160.3132-0.2268-0.1450.45760.0307-0.2115-0.05390.26380.0687-0.02860.31390.00480.326310.68535.458532.0477
111.6488-1.1707-0.94778.9724-2.841.98680.10480.1063-0.1365-0.1121-0.2035-0.38320.00110.30670.09170.2308-0.008-0.03020.35910.00810.300613.029826.050736.6371
128.4542.92791.43717.2294-0.7043.56370.22220.15950.5177-0.7355-0.21281.49030.3181-0.8232-0.15520.53030.0141-0.01360.45370.0050.31077.47332.06925.2229
132.24550.0319-0.24172.88720.57914.64440.00630.8002-0.0735-0.64180.1821-0.17320.17870.4277-0.20760.7160.05450.07840.6552-0.01140.372913.515445.73532.426
149.3563-2.5084.08174.55810.92133.36890.3855-0.2312-0.882-0.6135-0.05861.65711.5478-0.0236-0.35040.824-0.0931-0.06310.52740.00280.5554-0.981238.34318.5733
153.58490.3242-1.38792.27821.07964.54630.0710.40680.358-0.39150.1506-0.0837-0.36330.2432-0.2140.54930.01820.01480.43530.07950.39917.8754.403111.4521
165.47840.47490.76825.18430.34961.41550.4507-0.4385-0.79830.1844-0.3829-1.3480.14450.53370.01090.3039-0.0367-0.04820.56270.07210.741749.816648.320548.8614
176.04990.10830.45555.4201-0.39583.02530.0485-0.75350.19360.7025-0.2326-0.3335-0.32740.33720.10320.473-0.1210.01040.54070.01120.452939.565959.474553.9201
185.38041.66991.66723.73531.9273.18030.0894-0.16180.5971-0.254-0.26690.3826-0.5724-0.19240.23760.3661-0.00790.0490.38120.03010.536729.999761.790544.8746
195.96221.15580.85743.44951.67563.07020.21860.24650.68840.0623-0.1151-0.3686-0.09920.8363-0.23490.5092-0.16540.08160.49480.09020.538645.591865.202546.241
200.8073-0.4466-0.46915.7708-1.11271.39030.030.6699-0.2041-0.8188-0.4279-0.74230.14820.66890.53180.4740.00340.10950.7815-0.00010.520541.405149.454232.939
215.88924.2395-0.66359.1171-2.05065.04780.6768-0.5607-0.75220.884-0.6507-0.5380.61250.5763-0.02840.6313-0.1257-0.15970.65920.20130.672341.083142.713256.4187
225.08461.75060.53285.451.00883.48850.2440.6734-0.4654-0.35960.0716-0.65610.09820.3413-0.0530.40470.06350.0830.4409-0.04580.458236.299443.61236.583
235.24712.0270.40996.92140.20884.85370.2673-0.1427-1.0230.096-0.2921-1.00520.5213-0.018-0.06180.3884-0.007-0.00740.51550.06090.677637.662241.230846.1386
245.26242.76490.75396.63690.34153.5690.05430.3729-0.3885-0.1245-0.0719-0.43590.02960.23810.03260.27490.0580.00790.3717-0.00950.433536.124645.529640.5443
254.65271.01950.71667.9334-0.46925.0191-0.09790.40250.5182-1.3398-0.12690.2871-0.56840.55510.1390.4576-0.06280.04780.47270.0680.39335.403360.474135.781
263.9421-0.5146-0.64723.27270.28264.9513-0.1085-0.2747-0.02490.48910.230.5138-0.31650.109-0.13210.47820.00630.23890.36450.0180.5681-0.855645.532180.7075
274.6227-0.48095.36193.08452.41349.5894-0.14480.66771.1298-0.3980.22190.6582-1.67321.3156-0.02230.8033-0.05970.17420.60060.09330.78532.814759.596771.5078
284.25320.3301-1.25332.9061-0.06085.6964-0.00090.59250.0555-0.18830.09740.8995-0.2292-0.8055-0.06710.43170.07280.08190.51330.00820.7658-8.871545.35369.5469
290.8072.34710.22948.41591.64332.40320.0068-0.04570.21070.0990.4206-0.4518-0.5640.5278-0.38840.4022-0.0890.11820.5445-0.15050.44314.945947.989365.7559
308.011-0.06170.12155.80672.2498.4903-0.0893-0.5273-0.1691-0.15040.24670.345-0.4292-0.2069-0.18370.4184-0.05730.10890.3880.03830.4329.270345.949465.5034
317.14154.4208-3.87176.9736-1.62532.23620.0744-2.73590.26731.1064-0.8071-0.1470.08291.58770.79750.7561-0.14770.02711.2528-0.08860.539530.270748.364264.3905
325.37366.3169-6.14538.3288-6.7579.24510.2762-0.4017-0.17580.7861-0.4225-0.1834-0.44640.19650.10420.3876-0.01850.01770.35210.00150.38217.441740.647259.9598
336.4114.8379-0.03387.50640.23682.90030.05040.1550.4108-0.3295-0.05120.5966-0.15950.02080.04030.29620.01190.05390.2318-0.00430.263414.279945.91553.0378
348.42582.7053-2.02765.94440.82573.04860.1971-0.47250.03090.0154-0.17370.0642-0.11450.16980.0190.3482-0.01250.03080.32490.07590.245219.861548.538754.9953
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 29 through 42 )
2X-RAY DIFFRACTION2chain 'A' and (resid 43 through 95 )
3X-RAY DIFFRACTION3chain 'A' and (resid 96 through 137 )
4X-RAY DIFFRACTION4chain 'A' and (resid 138 through 154 )
5X-RAY DIFFRACTION5chain 'A' and (resid 155 through 188 )
6X-RAY DIFFRACTION6chain 'A' and (resid 189 through 246 )
7X-RAY DIFFRACTION7chain 'B' and (resid 371 through 393 )
8X-RAY DIFFRACTION8chain 'B' and (resid 394 through 400 )
9X-RAY DIFFRACTION9chain 'B' and (resid 401 through 416 )
10X-RAY DIFFRACTION10chain 'B' and (resid 417 through 444 )
11X-RAY DIFFRACTION11chain 'B' and (resid 445 through 456 )
12X-RAY DIFFRACTION12chain 'B' and (resid 457 through 468 )
13X-RAY DIFFRACTION13chain 'C' and (resid 29 through 154 )
14X-RAY DIFFRACTION14chain 'C' and (resid 155 through 168 )
15X-RAY DIFFRACTION15chain 'C' and (resid 169 through 246 )
16X-RAY DIFFRACTION16chain 'D' and (resid 29 through 42 )
17X-RAY DIFFRACTION17chain 'D' and (resid 43 through 95 )
18X-RAY DIFFRACTION18chain 'D' and (resid 96 through 117 )
19X-RAY DIFFRACTION19chain 'D' and (resid 118 through 137 )
20X-RAY DIFFRACTION20chain 'D' and (resid 138 through 154 )
21X-RAY DIFFRACTION21chain 'D' and (resid 155 through 168 )
22X-RAY DIFFRACTION22chain 'D' and (resid 169 through 188 )
23X-RAY DIFFRACTION23chain 'D' and (resid 189 through 203 )
24X-RAY DIFFRACTION24chain 'D' and (resid 204 through 228 )
25X-RAY DIFFRACTION25chain 'D' and (resid 229 through 246 )
26X-RAY DIFFRACTION26chain 'F' and (resid 29 through 154 )
27X-RAY DIFFRACTION27chain 'F' and (resid 155 through 168 )
28X-RAY DIFFRACTION28chain 'F' and (resid 169 through 246 )
29X-RAY DIFFRACTION29chain 'E' and (resid 371 through 380 )
30X-RAY DIFFRACTION30chain 'E' and (resid 381 through 393 )
31X-RAY DIFFRACTION31chain 'E' and (resid 394 through 400 )
32X-RAY DIFFRACTION32chain 'E' and (resid 401 through 416 )
33X-RAY DIFFRACTION33chain 'E' and (resid 417 through 444 )
34X-RAY DIFFRACTION34chain 'E' and (resid 445 through 468 )

+
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