[English] 日本語
Yorodumi
- PDB-9e83: TMPRSS2 crystal structure following acylation by UCSF_157 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9.0E+83
TitleTMPRSS2 crystal structure following acylation by UCSF_157
Components(Transmembrane protease serine ...) x 2
KeywordsHYDROLASE / trypsin-like serine protease / antiviral target / viral entry
Function / homology
Function and homology information


transmembrane protease serine 2 / symbiont-mediated induction of syncytium formation / 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 ...transmembrane protease serine 2 / symbiont-mediated induction of syncytium formation / 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 profile. / SRCR-like domain superfamily / Scavenger receptor Cys-rich / SRCR domain / 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 ...Scavenger receptor cysteine-rich domain / SRCR domain profile. / SRCR-like domain superfamily / Scavenger receptor Cys-rich / SRCR domain / 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 / 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
CITRIC ACID / 4-(2-aminoethyl)benzoic acid / Transmembrane protease serine 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07 Å
AuthorsFraser, B.J. / Dong, A. / Seitova, A. / Li, Y. / Hutchinson, A. / Young, N. / Bender, B. / Gahbauer, S. / Edwards, A. / Shoichet, B. ...Fraser, B.J. / Dong, A. / Seitova, A. / Li, Y. / Hutchinson, A. / Young, N. / Bender, B. / Gahbauer, S. / Edwards, A. / Shoichet, B. / Craik, C. / Arrowsmith, C.H.
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 4, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)40,6938
Polymers40,1492
Non-polymers5446
Water3,657203
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Elutes as single species on a gel filtration column
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2910 Å2
ΔGint-6 kcal/mol
Surface area14410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.853, 51.392, 64.625
Angle α, β, γ (deg.)90.00, 91.01, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
Transmembrane protease serine ... , 2 types, 2 molecules BA

#1: 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): modified pFASTBAC HTA baculovirus donor vector for secreted protein production from Sf9 insect cells
Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O15393
#2: Protein Transmembrane protease serine 2 non-catalytic chain


Mass: 12292.607 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): Derivative of pFASTBAC HTA baculovirus donor vector for secreted protein production from Sf9 insect cells
Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O15393

-
Non-polymers , 5 types, 209 molecules

#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-VU4 / 4-(2-aminoethyl)benzoic acid


Mass: 165.189 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H11NO2 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 1 / Source method: obtained synthetically / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 203 / Source method: isolated from a natural source / Formula: H2O

-
Details

Compound detailsTMPRSS2 catalytic chain linked to the non-catalytic chain through a C244-C365 disulfide bond after ...TMPRSS2 catalytic chain linked to the non-catalytic chain through a C244-C365 disulfide bond after the protease is activated.
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.53 Å3/Da / Density % sol: 51.45 % / Description: 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

-
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
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.06→40 Å / Num. obs: 23755 / % possible obs: 96.3 % / Redundancy: 5.1 % / CC1/2: 0.93 / CC star: 0.982 / Rmerge(I) obs: 0.233 / Rpim(I) all: 0.11 / Rrim(I) all: 0.259 / Χ2: 2.249 / Net I/σ(I): 4.1 / Num. measured all: 121196
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.06-2.14.10.94210490.5480.8410.4761.0610.64686.1
2.1-2.134.40.84110830.6650.8940.4040.9370.57888.7
2.13-2.174.60.77511180.6990.9070.3690.8620.59590.7
2.17-2.224.80.71711380.7610.930.3350.7950.63894
2.22-2.274.80.73111610.6910.9040.3520.8150.80694.9
2.27-2.3250.59311850.8530.960.2780.6570.68696.5
2.32-2.3850.52912020.860.9620.250.5870.7398.2
2.38-2.4450.511990.8840.9690.2360.5550.70798.1
2.44-2.514.80.46411670.8920.9710.2230.5170.84295.3
2.51-2.65.50.44412050.9220.9790.2030.4890.8798.9
2.6-2.695.70.37412430.9340.9830.1680.4110.9699.4
2.69-2.85.70.33912130.9320.9820.1550.3741.0599.3
2.8-2.925.70.3112190.9480.9860.1430.3421.1598.8
2.92-3.085.50.2412190.9670.9920.1110.2651.50598.9
3.08-3.275.30.20812140.9660.9910.0970.232.17298.9
3.27-3.525.20.18312010.9660.9910.0880.2043.09197.9
3.52-3.8850.17112110.9590.990.0820.194.85196.9
3.88-4.445.20.17212230.9610.990.0820.1917.26798.3
4.44-5.595.20.15512260.9510.9870.0740.1737.20897.3
5.59-405.30.13712790.9750.9940.0610.156.58998.5

-
Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
HKL-3000data scaling
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.07→39.29 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.916 / SU B: 7.693 / SU ML: 0.191 / Cross valid method: THROUGHOUT / ESU R: 0.204 / ESU R Free: 0.191 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25991 1128 4.8 %RANDOM
Rwork0.20004 ---
obs0.20294 22613 96.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.376 Å2
Baniso -1Baniso -2Baniso -3
1-4.65 Å20 Å21.27 Å2
2---2.81 Å20 Å2
3----1.88 Å2
Refinement stepCycle: 1 / Resolution: 2.07→39.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2436 0 37 203 2676
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0112572
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162258
X-RAY DIFFRACTIONr_angle_refined_deg1.5011.6343508
X-RAY DIFFRACTIONr_angle_other_deg0.5391.5565243
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.765331
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.99558
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.23910373
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0750.2383
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022913
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02521
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_it3.514.0121299
X-RAY DIFFRACTIONr_mcbond_other3.4544.0141299
X-RAY DIFFRACTIONr_mcangle_it5.065.9761616
X-RAY DIFFRACTIONr_mcangle_other5.0675.981617
X-RAY DIFFRACTIONr_scbond_it4.0544.1571273
X-RAY DIFFRACTIONr_scbond_other4.0554.1521272
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.9756.1261886
X-RAY DIFFRACTIONr_long_range_B_refined8.20850.5413006
X-RAY DIFFRACTIONr_long_range_B_other8.20750.5683007
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.07→2.121 Å
RfactorNum. reflection% reflection
Rfree0.274 64 -
Rwork0.309 1487 -
obs--86.07 %

+
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