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- EMDB-22252: CRYOEM STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS ZINC METALLOPROTEA... -

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Basic information

Entry
Database: EMDB / ID: EMD-22252
TitleCRYOEM STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS ZINC METALLOPROTEASE ZMP1 IN OPEN STATE
Map dataZINC METALLOPROTEASE ZMP1 IN OPEN STATE
Sample
  • Organelle or cellular component: MYCOBACTERIUM TUBERCULOSIS ZINC METALLOPROTEASE
    • Protein or peptide: Probable zinc metalloprotease Zmp1
  • Ligand: ZINC ION
KeywordsOpen state / HYDROLASE
Function / homology
Function and homology information


metalloendopeptidase activity / protein processing / metal ion binding / plasma membrane
Similarity search - Function
Peptidase M13 / Peptidase M13, N-terminal domain / Peptidase M13, C-terminal domain / Peptidase M13, domain 2 / Peptidase family M13 / Peptidase family M13 / Neprilysin-like (M13) protease domain profile. / Metallopeptidase, catalytic domain superfamily
Similarity search - Domain/homology
Probable zinc metalloprotease Zmp1
Similarity search - Component
Biological speciesMycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsLiang WG / Zhao M
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Aging (NIH/NIA)R01 GM121964 United States
CitationJournal: Structure / Year: 2021
Title: Structural analysis of Mycobacterium tuberculosis M13 metalloprotease Zmp1 open states.
Authors: Wenguang G Liang / Jordan M Mancl / Minglei Zhao / Wei-Jen Tang /
Abstract: Zinc metalloprotease 1 (Zmp1), a Mycobacterium tuberculosis 75 kDa secreted enzyme, mediates key stages of tuberculosis disease progression. The biological activity of Zmp1 presumably stems from its ...Zinc metalloprotease 1 (Zmp1), a Mycobacterium tuberculosis 75 kDa secreted enzyme, mediates key stages of tuberculosis disease progression. The biological activity of Zmp1 presumably stems from its ability to degrade bacterium- and/or host-derived peptides. The crystal structures of Zmp1 and related M13 metalloproteases, such as neprilysin and endothelin-converting enzyme-1 were determined only in the closed conformation, which cannot capture substrates or release proteolytic products. Thus, the mechanisms of substrate binding and selectivity remain elusive. Here we report two open-state cryo-EM structures of Zmp1, revealed by our SAXS analysis to be the dominant states in solution. Our structural analyses reveal how ligand binding induces a conformational switch in four linker regions to drive the rigid body motion of the D1 and D2 domains, which form the sizable catalytic chamber. Furthermore, they offer insights into the catalytic cycle and mechanism of substrate recognition of M13 metalloproteases for future therapeutic innovations.
History
DepositionJun 29, 2020-
Header (metadata) releaseDec 23, 2020-
Map releaseDec 23, 2020-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6xly
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22252.png

Downloads & links

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Map

FileDownload / File: emd_22252.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationZINC METALLOPROTEASE ZMP1 IN OPEN STATE
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 192 pix.
= 204.096 Å		1.06 Å/pix.
x 192 pix.
= 204.096 Å		1.06 Å/pix.
x 192 pix.
= 204.096 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.063 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02 / Movie #1: 0.02
Minimum - Maximum-0.031569924 - 0.084406264
Average (Standard dev.)-0.0000005349951 (±0.0024036167)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions192192192
Spacing192192192
CellA=B=C: 204.096 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0631.0631.063
M x/y/z192192192
origin x/y/z0.0000.0000.000
length x/y/z204.096204.096204.096
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS192192192
D min/max/mean-0.0320.084-0.000

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Supplemental data

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Mask #1

Fileemd_22252_msk_1.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Additional map: sharpen map

Fileemd_22252_additional_1.map
Annotationsharpen map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: ZINC METALLOPROTEASE ZMP1 IN OPEN STATE

Fileemd_22252_half_map_1.map
AnnotationZINC METALLOPROTEASE ZMP1 IN OPEN STATE
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: ZINC METALLOPROTEASE ZMP1 IN OPEN STATE

Fileemd_22252_half_map_2.map
AnnotationZINC METALLOPROTEASE ZMP1 IN OPEN STATE
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : MYCOBACTERIUM TUBERCULOSIS ZINC METALLOPROTEASE

EntireName: MYCOBACTERIUM TUBERCULOSIS ZINC METALLOPROTEASE
Components
  • Organelle or cellular component: MYCOBACTERIUM TUBERCULOSIS ZINC METALLOPROTEASE
    • Protein or peptide: Probable zinc metalloprotease Zmp1
  • Ligand: ZINC ION

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Supramolecule #1: MYCOBACTERIUM TUBERCULOSIS ZINC METALLOPROTEASE

SupramoleculeName: MYCOBACTERIUM TUBERCULOSIS ZINC METALLOPROTEASE / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv

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Macromolecule #1: Probable zinc metalloprotease Zmp1

MacromoleculeName: Probable zinc metalloprotease Zmp1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv
Molecular weightTheoretical: 78.132953 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MRGSHHHHHH GMASMTGGQQ MGRDLYDDDD KDHPFTMTLA IPSGIDLSHI DADARPQDDL FGHVNGRWLA EHEIPADRAT DGAFRSLFD RAETQVRDLI IQASQAGAAV GTDAQRIGDL YASFLDEEAV ERAGVQPLHD ELATIDSAAD ATELAAALGT L QRAGVGGG ...String:
MRGSHHHHHH GMASMTGGQQ MGRDLYDDDD KDHPFTMTLA IPSGIDLSHI DADARPQDDL FGHVNGRWLA EHEIPADRAT DGAFRSLFD RAETQVRDLI IQASQAGAAV GTDAQRIGDL YASFLDEEAV ERAGVQPLHD ELATIDSAAD ATELAAALGT L QRAGVGGG IGVYVDTDSK DSTRYLVHFT QSGIGLPDES YYRDEQHAAV LAAYPGHIAR MFGLVYGGES RDHAKTADRI VA LETKLAD AHWDVVKRRD ADLGYNLRTF AQLQTEGAGF DWVSWVTALG SAPDAMTELV VRQPDYLVTF ASLWASVNVE DWK CWARWR LIRARAPWLT RALVAEDFEF YGRTLTGAQQ LRDRWKRGVS LVENLMGDAV GKLYVQRHFP PDAKSRIDTL VDNL QEAYR ISISELDWMT PQTRQRALAK LNKFTAKVGY PIKWRDYSKL AIDRDDLYGN VQRGYAVNHD RELAKLFGPV DRDEW FMTP QTVNAYYNPG MNEIVFPAAI LQPPFFDPQA DEAANYGGIG AVIGHEIGHG FDDQGAKYDG DGNLVDWWTD DDRTEF AAR TKALIEQYHA YTPRDLVDHP GPPHVQGAFT IGENIGDLGG LSIALLAYQL SLNGNPAPVI DGLTGMQRVF FGWAQIW RT KSRAAEAIRR LAVDPHSPPE FRCNGVVRNV DAFYQAFDVT EDDALFLDPQ RRVRIWN

UniProtKB: Probable zinc metalloprotease Zmp1

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Macromolecule #2: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 2 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.8 mg/mL
BufferpH: 6.8
Details: 20 mM HEPES (pH 6.8), 150 mM NaCl, 0.5 mM bMe, 20 mM Trimethylamine N-oxide dihydrate
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 308 K / Instrument: FEI VITROBOT MARK II

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average exposure time: 5.0 sec. / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.8000000000000003 µm / Nominal defocus min: 1.4000000000000001 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 541716
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
FSC plot (resolution estimation)

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