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- PDB-8v04: High resolution TMPRSS2 structure following acylation by nafamostat -

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Basic information

Entry
Database: PDB / ID: 8v04
TitleHigh resolution TMPRSS2 structure following acylation by nafamostat
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
CITRIC ACID / 4-carbamimidamidobenzoic acid / Transmembrane protease serine 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å
AuthorsFraser, B.J. / Dong, A. / Kutera, M. / Seitova, A. / Li, Y. / Hutchinson, A. / Edwards, A. / Benard, F. / Levon, H. / Arrowsmith, C.
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: High resolution TMPRSS2 structure following acylation by nafamostat
Authors: Fraser, B.J. / Dong, A. / Kutera, M. / Seitova, A. / Li, Y. / Hutchinson, A. / Edwards, A. / Benard, F. / Levon, H. / Arrowsmith, C.
History
DepositionNov 16, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 31, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,23817
Polymers40,1212
Non-polymers2,11715
Water5,765320
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4690 Å2
ΔGint10 kcal/mol
Surface area16440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.757, 50.502, 64.578
Angle α, β, γ (deg.)90.00, 91.60, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Transmembrane protease serine ... , 2 types, 2 molecules AB

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


Mass: 12264.598 Da / Num. of mol.: 1 / Mutation: S251D, R252D, Q253D, S254D, R255K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TMPRSS2, PRSS10 / Plasmid: pFHMSP-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.: 1 / 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 , 1 types, 1 molecules

#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(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: 773.734 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-1-2/a4-b1_a6-d1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE

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Non-polymers , 7 types, 334 molecules

#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
Formula: C2H6O2
#5: Chemical ChemComp-UNX / UNKNOWN ATOM OR ION


Mass: 179.176 Da / Num. of mol.: 1 / Source method: obtained synthetically
#6: Chemical ChemComp-GBS / 4-carbamimidamidobenzoic acid / Nafamostat, bound form


Mass: 179.176 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H9N3O2 / Feature type: SUBJECT OF INVESTIGATION
Comment: anticancer, anticoagulant, antivirus, protease inhibitor*YM
#7: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#8: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Ca
#9: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 320 / 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: 2.52 Å3/Da / Density % sol: 51.28 % / Description: Hexagonal plates
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 3 uL hanging drop (2:1 protein:precipitant) grown over precipitant solution containing 25%PEG4000, 0.2M ammonium sulfate, and 0.1M sodium acetate pH 4.6. Protein (10 mg/mL) was in a buffer ...Details: 3 uL hanging drop (2:1 protein:precipitant) grown over precipitant solution containing 25%PEG4000, 0.2M ammonium sulfate, and 0.1M sodium acetate pH 4.6. Protein (10 mg/mL) was in a buffer containing 25 mM Tris pH 8.0, 75 mM NaCl, and 2 mM CaCl2

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: cryo cooled / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Mar 19, 2022
RadiationMonochromator: Cryo-cooled double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.58→40 Å / Num. obs: 94364 / % possible obs: 92.8 % / Redundancy: 2.2 % / CC1/2: 0.988 / CC star: 0.997 / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.079 / Rrim(I) all: 0.127 / Χ2: 2.246 / Net I/σ(I): 8.7 / Num. measured all: 212101
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.58-1.612.20.66345570.6250.8770.5280.8510.48191.6
1.61-1.642.20.62746670.6640.8930.50.8050.48591.6
1.64-1.672.20.54846940.7430.9230.4360.7030.4891.9
1.67-1.72.20.49246480.7640.9310.3920.6310.5191.7
1.7-1.742.20.41246900.8170.9480.3270.5280.54891.7
1.74-1.782.20.34646160.8610.9620.2760.4440.54991.2
1.78-1.822.20.29746040.890.970.2360.3810.64390.8
1.82-1.872.20.25646130.9070.9750.2040.3280.78790.5
1.87-1.932.10.21944860.930.9820.1780.2830.81288.5
1.93-1.992.10.1844100.9410.9850.1450.2321.10186.6
1.99-2.062.30.15947640.9570.9890.1270.2041.16293.9
2.06-2.142.30.13348770.9680.9920.1050.171.52695.5
2.14-2.242.30.1248080.9710.9930.0950.1541.78195.1
2.24-2.362.30.10348960.9790.9950.0820.1332.06595.8
2.36-2.512.30.10248750.9740.9930.0820.1322.61695.5
2.51-2.72.30.09348820.9780.9940.0750.123.24495.8
2.7-2.972.30.08848270.980.9950.070.1134.29994.7
2.97-3.42.20.07547420.9820.9960.0590.0966.16493.3
3.4-4.292.20.05547460.990.9980.0430.077.59493.2
4.29-402.40.04749620.9940.9990.0350.0596.23197.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
HKL-3000data scaling
HKL-3000data reduction
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.58→39.81 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.96 / SU B: 1.615 / SU ML: 0.056 / Cross valid method: THROUGHOUT / ESU R: 0.075 / ESU R Free: 0.075 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18084 2463 4.8 %RANDOM
Rwork0.15571 ---
obs0.15695 49216 99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.803 Å2
Baniso -1Baniso -2Baniso -3
1-2.51 Å2-0 Å20.88 Å2
2---0.25 Å20 Å2
3----2.31 Å2
Refinement stepCycle: 1 / Resolution: 1.58→39.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2614 0 128 320 3062
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0123001
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162666
X-RAY DIFFRACTIONr_angle_refined_deg1.6591.6484108
X-RAY DIFFRACTIONr_angle_other_deg0.5961.5586264
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7325403
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.446512
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.82410464
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0850.2449
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023408
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02600
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_it2.0791.9711430
X-RAY DIFFRACTIONr_mcbond_other2.0771.971430
X-RAY DIFFRACTIONr_mcangle_it3.1232.9431801
X-RAY DIFFRACTIONr_mcangle_other3.1252.9451802
X-RAY DIFFRACTIONr_scbond_it3.1132.3871571
X-RAY DIFFRACTIONr_scbond_other3.1122.3881572
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.643.4132276
X-RAY DIFFRACTIONr_long_range_B_refined6.88930.8643611
X-RAY DIFFRACTIONr_long_range_B_other6.88730.8623611
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.58→1.619 Å
RfactorNum. reflection% reflection
Rfree0.222 157 -
Rwork0.228 3491 -
obs--95.52 %

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