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- PDB-8v1f: TMPRSS2 complexed with the noncovalent inhibitor 6-amidino-2-napthol -

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Basic information

Entry
Database: PDB / ID: 8v1f
TitleTMPRSS2 complexed with the noncovalent inhibitor 6-amidino-2-napthol
Components(Transmembrane protease serine ...) x 2
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Inhibitor complex / protease / viral entry / Structural Genomics / Structural Genomics Consortium / SGC / HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


transmembrane protease serine 2 / protein autoprocessing / Attachment and Entry / serine-type peptidase activity / viral translation / Induction of Cell-Cell Fusion / Attachment and Entry / positive regulation of viral entry into host cell / serine-type endopeptidase activity / proteolysis ...transmembrane protease serine 2 / protein autoprocessing / Attachment and Entry / serine-type peptidase activity / viral translation / Induction of Cell-Cell Fusion / Attachment and Entry / positive regulation of viral entry into host cell / serine-type endopeptidase activity / proteolysis / extracellular exosome / extracellular region / nucleoplasm / plasma membrane
Similarity search - Function
Scavenger receptor cysteine-rich domain / SRCR domain / SRCR domain profile. / SRCR-like domain / SRCR-like domain superfamily / Scavenger receptor Cys-rich / Low-density lipoprotein (LDL) receptor class A, conserved site / LDL-receptor class A (LDLRA) domain signature. / LDL-receptor class A (LDLRA) domain profile. / Low-density lipoprotein receptor domain class A ...Scavenger receptor cysteine-rich domain / SRCR domain / SRCR domain profile. / SRCR-like domain / SRCR-like domain superfamily / Scavenger receptor Cys-rich / Low-density lipoprotein (LDL) receptor class A, conserved site / LDL-receptor class A (LDLRA) domain signature. / LDL-receptor class A (LDLRA) domain profile. / Low-density lipoprotein receptor domain class A / Low-density lipoprotein (LDL) receptor class A repeat / LDL receptor-like superfamily / 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 / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
6-oxidanylnaphthalene-2-carboximidamide / CITRIC ACID / DI(HYDROXYETHYL)ETHER / Transmembrane protease serine 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 Å
AuthorsFraser, B.J. / Dong, A. / Kutera, M. / Seitova, A. / Li, Y. / Hutchinson, A. / Edwards, A. / Benard, F. / Halabelian, L. / Arrowsmith, C. / Structural Genomics Consortium (SGC)
Funding support Canada, United States, 2items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)FDN154328 Canada
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30 GM124165 United States
CitationJournal: To Be Published
Title: TMPRSS2 complexed with the noncovalent inhibitor 6-amidino-2-napthol
Authors: Fraser, B.J. / Dong, A. / Kutera, M. / Seitova, A. / Li, Y. / Hutchinson, A. / Edwards, A. / Benard, F. / Halabelian, L. / Arrowsmith, C. / Structural Genomics Consortium (SGC)
History
DepositionNov 20, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 7, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transmembrane protease serine 2 non-catalytic chain
B: Transmembrane protease serine 2
C: Transmembrane protease serine 2 non-catalytic chain
D: Transmembrane protease serine 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,38340
Polymers80,2434
Non-polymers4,14036
Water5,585310
1
A: Transmembrane protease serine 2 non-catalytic chain
B: Transmembrane protease serine 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,96620
Polymers40,1212
Non-polymers1,84518
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4780 Å2
ΔGint13 kcal/mol
Surface area16260 Å2
MethodPISA
2
C: Transmembrane protease serine 2 non-catalytic chain
D: Transmembrane protease serine 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,41720
Polymers40,1212
Non-polymers2,29518
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6320 Å2
ΔGint36 kcal/mol
Surface area16030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.939, 172.573, 83.297
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11D-720-

HOH

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Components

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Transmembrane protease serine ... , 2 types, 4 molecules ACBD

#1: Protein Transmembrane protease serine 2 non-catalytic chain


Mass: 12264.598 Da / Num. of mol.: 2 / Fragment: SRCR domain non-catalytic chain residues 148-254 / Mutation: S251D, R252D, Q253D, S254D, R255K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TMPRSS2, PRSS10 / Plasmid: pFHSMP-LIC-C
Details (production host): baculovirus donor vector for secreted protein production
Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O15393
#2: Protein Transmembrane protease serine 2


Mass: 27856.742 Da / Num. of mol.: 2 / Fragment: Peptidase S1 domain residues 256-492
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TMPRSS2 / Plasmid: pFHMSP-LIC-C
Details (production host): baculovirus donor vector for secreted protein production
Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O15393

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Sugars , 2 types, 2 molecules

#3: 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.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam 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
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}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.: 1
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

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Non-polymers , 8 types, 344 molecules

#5: Chemical
ChemComp-TAM / TRIS(HYDROXYETHYL)AMINOMETHANE


Mass: 163.215 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C7H17NO3 / Comment: pH buffer*YM
#6: Chemical ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 3 / Source method: obtained synthetically
#7: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C2H6O2
#8: Chemical ChemComp-7R8 / 6-oxidanylnaphthalene-2-carboximidamide


Mass: 186.210 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H10N2O / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C4H10O3
#10: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#11: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#12: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 310 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.68 Å3/Da / Density % sol: 54.09 % / Description: 2D diamond shaped plates
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: precipitant containing 20% PEG3350, 0.2 M dibasic ammonium citrate. Protein mixed 1uL:1uL protein:precipitant and set as 2 uL hanging drop on glass slides
PH range: 4.8 to 5.3

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 11, 2022
RadiationMonochromator: Zr filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.19→40 Å / Num. obs: 44382 / % possible obs: 99.7 % / Redundancy: 9 % / CC1/2: 0.984 / CC star: 0.996 / Rmerge(I) obs: 0.226 / Rpim(I) all: 0.076 / Rrim(I) all: 0.239 / Χ2: 1.057 / Net I/σ(I): 5.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.2-2.246.82.74921990.2910.6711.1142.9750.44999.7
2.24-2.2872.1921820.3130.6910.8772.3650.48499.7
2.28-2.327.11.49822100.5750.8540.5971.6160.46999.6
2.32-2.3771.21421230.4180.7680.4851.3130.48798.1
2.37-2.428.11.2621780.7830.9370.4571.3430.47799.6
2.42-2.488.61.10622210.810.9460.3911.1740.50399.9
2.48-2.548.80.93622020.8720.9650.3260.9930.50699.9
2.54-2.6190.78122040.8970.9730.2710.8280.54399.9
2.61-2.6990.68122000.8850.9690.2340.7210.5699.9
2.69-2.779.20.6422300.8960.9720.2170.6770.59399.9
2.77-2.879.40.56621980.9570.9890.1890.5970.656100
2.87-2.999.70.47622250.9670.9920.1570.5020.722100
2.99-3.129.70.38322110.9710.9930.1270.4040.8799.9
3.12-3.299.60.322090.9840.9960.1010.3171.11899.8
3.29-3.498.90.25122110.9610.990.0870.2671.39599.1
3.49-3.7610.70.19622360.9920.9980.0620.2051.727100
3.76-4.1410.70.1622330.9940.9980.050.1682.006100
4.14-4.7410.60.12122570.9960.9990.0380.1272.29899.9
4.74-5.9710.50.10122850.9970.9990.0320.1061.837100
5.97-4010.10.06923680.9970.9990.0220.0721.79499.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
HKL-3000data scaling
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.19→38.67 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.945 / SU B: 7.001 / SU ML: 0.166 / Cross valid method: THROUGHOUT / ESU R: 0.204 / ESU R Free: 0.18 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22275 462 1 %RANDOM
Rwork0.17168 ---
obs0.17223 43904 99.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.183 Å2
Baniso -1Baniso -2Baniso -3
1--1.43 Å2-0 Å2-0 Å2
2--1.46 Å20 Å2
3----0.03 Å2
Refinement stepCycle: 1 / Resolution: 2.19→38.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5319 0 280 310 5909
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0125748
X-RAY DIFFRACTIONr_bond_other_d0.0010.0165022
X-RAY DIFFRACTIONr_angle_refined_deg1.5741.6547793
X-RAY DIFFRACTIONr_angle_other_deg0.5181.55711682
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1985697
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.016520
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.51910800
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0730.2841
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.026411
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021145
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_it3.7764.1562780
X-RAY DIFFRACTIONr_mcbond_other3.7764.1552779
X-RAY DIFFRACTIONr_mcangle_it5.296.2173465
X-RAY DIFFRACTIONr_mcangle_other5.2896.2183466
X-RAY DIFFRACTIONr_scbond_it4.734.7482968
X-RAY DIFFRACTIONr_scbond_other4.7294.7492969
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.8516.9294325
X-RAY DIFFRACTIONr_long_range_B_refined8.67955.3076629
X-RAY DIFFRACTIONr_long_range_B_other8.67855.316630
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.19→2.244 Å
RfactorNum. reflection% reflection
Rfree0.301 29 -
Rwork0.315 3102 -
obs--96.88 %

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