[English] 日本語
Yorodumi
- PDB-9jd0: Crystal structure of TMPRSS2 in complex with nanobody -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9jd0
TitleCrystal structure of TMPRSS2 in complex with nanobody
Components
  • (Transmembrane protease serine 2 ...) x 2
  • Nanobody
KeywordsANTIVIRAL PROTEIN / Complex / Antibody / Host protease
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 / entry receptor-mediated virion attachment to host cell / Attachment and Entry / positive regulation of viral entry into host cell / serine-type endopeptidase activity ...transmembrane protease serine 2 / protein autoprocessing / Attachment and Entry / serine-type peptidase activity / viral translation / Induction of Cell-Cell Fusion / entry receptor-mediated virion attachment to host cell / 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
MALONATE ION / Transmembrane protease serine 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Vicugna pacos (alpaca)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsWang, H. / Zhao, Z. / Liu, X. / Duan, Y. / Yang, H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)92169109 China
CitationJournal: Nat Commun / Year: 2025
Title: The crystal structure of coronavirus RBD-TMPRSS2 complex provides basis for the discovery of therapeutic antibodies.
Authors: Zhao, Z. / Yang, Q. / Liu, X. / Li, M. / Duan, Y. / Du, M. / Zhou, A. / Liu, H. / He, Y. / Wang, W. / Lu, Y. / Zhang, X. / Wang, H. / Yang, X. / Zhang, H. / Chen, X. / Rao, Z. / Yang, H.
History
DepositionAug 30, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 30, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)118,25415
Polymers117,2316
Non-polymers1,0239
Water12,448691
1
A: Transmembrane protease serine 2 non-catalytic chain
C: Transmembrane protease serine 2 catalytic chain
E: Nanobody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,1738
Polymers58,6163
Non-polymers5575
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5520 Å2
ΔGint-10 kcal/mol
Surface area21240 Å2
MethodPISA
2
B: Transmembrane protease serine 2 non-catalytic chain
D: Transmembrane protease serine 2 catalytic chain
F: Nanobody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,0817
Polymers58,6163
Non-polymers4654
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5390 Å2
ΔGint-8 kcal/mol
Surface area20940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.547, 137.547, 130.325
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

-
Components

-
Transmembrane protease serine 2 ... , 2 types, 4 molecules ABCD

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


Mass: 16054.661 Da / Num. of mol.: 2 / Mutation: S250D,S251D,R252D,Q253D, S254K
Source method: isolated from a genetically manipulated source
Details: We choose the ectodomain of transmembrane protease serine 2 (residues: 109-492) for expression. Residues 250-255 responsible for autocleavage are substituted with DDDDK. The recombinant ...Details: We choose the ectodomain of transmembrane protease serine 2 (residues: 109-492) for expression. Residues 250-255 responsible for autocleavage are substituted with DDDDK. The recombinant protein was cleaved into two chains (A and C) in the purification.
Source: (gene. exp.) Homo sapiens (human) / Gene: TMPRSS2, PRSS10 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O15393
#2: Protein Transmembrane protease serine 2 catalytic chain


Mass: 27856.742 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: We choose the ectodomain of transmembrane protease serine 2 (residues: 109-492) for expression. Residues 250-255 responsible for autocleavage are substituted with DDDDK. The recombinant ...Details: We choose the ectodomain of transmembrane protease serine 2 (residues: 109-492) for expression. Residues 250-255 responsible for autocleavage are substituted with DDDDK. The recombinant protein was cleaved into two chains (A and C) in the purification.
Source: (gene. exp.) Homo sapiens (human) / Gene: TMPRSS2, PRSS10 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O15393

-
Antibody / Sugars , 2 types, 4 molecules FE

#3: Antibody Nanobody


Mass: 14704.325 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The recombinant protein encompasses a C-terminal linker ("GS") followed by a 6 x His tag.
Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Homo sapiens (human)
#5: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

-
Non-polymers , 4 types, 698 molecules

#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical
ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H2O4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 691 / 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: 2.63 Å3/Da / Density % sol: 53.21 %
Crystal growTemperature: 293 K / Method: evaporation
Details: 0.2 M sodium malonate pH 6.0, 10% (w/v) Polyethylene glycol 3,350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Apr 14, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2→43.5 Å / Num. obs: 84570 / % possible obs: 99.9 % / Redundancy: 14.97 % / CC1/2: 0.999 / Rmerge(I) obs: 0.106 / Rrim(I) all: 0.11 / Net I/σ(I): 19.63
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
2-2.120.883134310.90.9151
2.12-2.270.581127040.9550.6011
2.27-2.450.375118430.9820.3881
2.45-2.680.246109420.9910.2551
2.68-30.14699430.9970.1511
3-3.460.08388140.9980.0861
3.46-4.230.05875180.9990.061
4.23-5.960.05159070.9990.0531
5.96-43.50.04634670.9990.0481

-
Processing

Software
NameVersionClassification
PHENIX(1.21_5207-000)refinement
XDSdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→43.5 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2205 4224 5 %
Rwork0.188 --
obs0.1896 84501 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→43.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7613 0 64 691 8368
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0047960
X-RAY DIFFRACTIONf_angle_d0.69210837
X-RAY DIFFRACTIONf_dihedral_angle_d14.652852
X-RAY DIFFRACTIONf_chiral_restr0.0521151
X-RAY DIFFRACTIONf_plane_restr0.0061415
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.020.3081370.26772612X-RAY DIFFRACTION98
2.02-2.050.27281370.23962615X-RAY DIFFRACTION100
2.05-2.070.26391410.2272666X-RAY DIFFRACTION100
2.07-2.10.25811370.23212610X-RAY DIFFRACTION100
2.1-2.120.28511400.21452658X-RAY DIFFRACTION100
2.12-2.150.28511400.2212662X-RAY DIFFRACTION100
2.15-2.180.24671390.21792635X-RAY DIFFRACTION100
2.18-2.220.27381380.21612633X-RAY DIFFRACTION100
2.22-2.250.26431410.21312673X-RAY DIFFRACTION100
2.25-2.290.27071400.20942657X-RAY DIFFRACTION100
2.29-2.330.22771390.19692642X-RAY DIFFRACTION100
2.33-2.370.22871390.20712650X-RAY DIFFRACTION100
2.37-2.420.24631400.21152663X-RAY DIFFRACTION100
2.42-2.470.26411400.21872644X-RAY DIFFRACTION100
2.47-2.520.27561390.22182653X-RAY DIFFRACTION100
2.52-2.580.2411400.21222656X-RAY DIFFRACTION100
2.58-2.640.2711410.20962674X-RAY DIFFRACTION100
2.64-2.710.26461400.19992674X-RAY DIFFRACTION100
2.71-2.790.23451410.20692663X-RAY DIFFRACTION100
2.79-2.880.23741400.1962664X-RAY DIFFRACTION100
2.88-2.990.23991410.20152690X-RAY DIFFRACTION100
2.99-3.110.24881420.20322684X-RAY DIFFRACTION100
3.11-3.250.20291400.18512674X-RAY DIFFRACTION100
3.25-3.420.20261420.18332698X-RAY DIFFRACTION100
3.42-3.630.21111430.1712710X-RAY DIFFRACTION100
3.63-3.910.19361420.16322702X-RAY DIFFRACTION100
3.91-4.310.18031440.15162726X-RAY DIFFRACTION100
4.31-4.930.15711440.14182747X-RAY DIFFRACTION100
4.93-6.210.17761460.17182777X-RAY DIFFRACTION100
6.21-43.50.22631510.19582878X-RAY DIFFRACTION98

+
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