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- EMDB-19403: Single-particle cryo-EM of the P1-P40P90 heterodimer from Mycopla... -

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Basic information

Entry
Database: EMDB / ID: EMD-19403
TitleSingle-particle cryo-EM of the P1-P40P90 heterodimer from Mycoplasma pneumoniae below 10 Angstrom resolution.
Map data
Sample
  • Complex: Single particle Cryo-EM of Heterodimer P1-P40/P90 from Mycoplasma pneumoniae
    • Protein or peptide: Heterodimer P1-P40P90 from Mycoplasma pneumoniae
KeywordsAdhesion / Heterodimer / P1 / P40P90 / Mycoplasma pneumoniae / CELL ADHESION
Biological speciesMycoplasmoides pneumoniae M129 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 12.0 Å
AuthorsKawamoto A / Vizarraga D / Marcos-Silva M / Fita I / Miyata M / Pinyol J / Namba K / Kenri T
Funding support Spain, Japan, 2 items
OrganizationGrant numberCountry
Ministerio de Ciencia e Innovacion (MCIN)PID2021-125632OB-C22, PID2021-125632OB-C21 Spain
Ministry of Education, Culture, Sports, Science and Technology (Japan)22K07063 Japan
CitationJournal: Biorxiv / Year: 2023
Title: Antibodies halting motility in Mycoplasma pneumoniae reveal the dynamic nature of the adhesion complex
Authors: Kawamoto A / Vizarraga D / Marcos-Silva M / Martin J / Makino F / Miyata T / Roel J / Marcos E / Aparicio D / Fita I / Miyata M / Pinol J / Namba K / Kenri T
History
DepositionJan 12, 2024-
Header (metadata) releaseFeb 5, 2025-
Map releaseFeb 5, 2025-
UpdateFeb 5, 2025-
Current statusFeb 5, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19403.png

Downloads & links

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Map

FileDownload / File: emd_19403.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)X (Row.)Y (Col.)
0.87 Å/pix.
x 288 pix.
= 250.56 Å		0.87 Å/pix.
x 288 pix.
= 250.56 Å		0.87 Å/pix.
x 288 pix.
= 250.56 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.87 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.06
Minimum - Maximum-0.4108133 - 1.0548432
Average (Standard dev.)0.0015921866 (±0.035219036)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderYXZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 250.56 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_19403_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_19403_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Single particle Cryo-EM of Heterodimer P1-P40/P90 from Mycoplasma...

EntireName: Single particle Cryo-EM of Heterodimer P1-P40/P90 from Mycoplasma pneumoniae
Components
  • Complex: Single particle Cryo-EM of Heterodimer P1-P40/P90 from Mycoplasma pneumoniae
    • Protein or peptide: Heterodimer P1-P40P90 from Mycoplasma pneumoniae

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Supramolecule #1: Single particle Cryo-EM of Heterodimer P1-P40/P90 from Mycoplasma...

SupramoleculeName: Single particle Cryo-EM of Heterodimer P1-P40/P90 from Mycoplasma pneumoniae
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Heterodimer formed by a subunit of P1 and another of P40/P90 that make up the Nap complex essential for adhesion in Mycoplasma pneumoniae
Source (natural)Organism: Mycoplasmoides pneumoniae M129 (bacteria)
Molecular weightTheoretical: 250 KDa

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Macromolecule #1: Heterodimer P1-P40P90 from Mycoplasma pneumoniae

MacromoleculeName: Heterodimer P1-P40P90 from Mycoplasma pneumoniae / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycoplasmoides pneumoniae M129 (bacteria)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: SLANTYLLQD HNTLTPYTPF TTPLNGGLDV VRAAHLHPSY ELVDWKRVGD TKLVALVRSA LVRVKFQDTT SSDQSNTNQN ALSFDTQESQ KALNGSNSQD FASYVLIFKA APRATWVFER KIKLALPYVK QESQGKGSLY KTLQDLLVEQ PVTPYTPNAG LARVNGVAQD ...String:
SLANTYLLQD HNTLTPYTPF TTPLNGGLDV VRAAHLHPSY ELVDWKRVGD TKLVALVRSA LVRVKFQDTT SSDQSNTNQN ALSFDTQESQ KALNGSNSQD FASYVLIFKA APRATWVFER KIKLALPYVK QESQGKGSLY KTLQDLLVEQ PVTPYTPNAG LARVNGVAQD TVHFGSGQES SWNSQRSQKG LKNNPGPKAV TGFKLDKGRA YRKLNESWPV YEPLDSTKEG KGKDESSWKN SEKTTAENDA PLVGATFSKY LNTAQALHQM GVIVPGLEKW TDALPNVITQ LYHTSTAQLA YLNGQIVVMG SDRVPSLWYW VVGEDQESGK ATWWAKTELN WGTDKQKQFV ENQLGFKDDS NSDSKNSNLK AQGLTQPAYL IAGLDVVADH LVFAAFKAGA VGYDMTTDSS ASTYNQALAW STTAGLDSDG GYKALVENTA GLNGPINGLF TLLDTFAYVT PVSGMKGGSQ NNEEVQTTYP VKSDQKATAK IASLINASPL NSYGDDGVTV FDALGLNFNF KLNEERLPSR TDQLLVYGIV NESELKSARE NAQSTSDDNS NTKVKWTNTA SHYLPVPYYY SANFPEAGNR RRGVKISTLE SQATDGFANS LLNFGTGLKA GVDPAPVARG HKPNYSAVLL VRGGVVRLNF NPDTDKLLDS TDKNSEPISF SYTPFGSAES AVDLTTLKDV TYIAESGLWF YTFDNGEKPT YDGKQQQVKN RKGYAVITVS RTGIEFNEDA NTTTLSQAPA ALAVQNGIAS SQDDLTGILP LSDEFSAVIT KDQTWTGKVD IYKNTNGLFE KDDQLSENVK RRNAINPRLT PWTYRNTSFS SLPLTGENPG AWALVRDNSA KGITSQQTTY DPTRTEAALT ASTTFALRRY DLAGRALYDL DFSKLNPQTP TRDQTGQITF NPFGGFGLSG AAPQQWNEVK NKVPVEVAQD PSNPYRFAVL LVPRSVVYYE QLQRGLGLPQ QRTESGSTTG AMFGLKVKNA EADTAKSNEK LQGASGQSTQ RGKVKALKIE VKKKSDSGQL QLEKNDLANA PIKRSEESGQ SVQLKADDFG TALSPTPWRP WLATEQIHKD LPKWSASILI LYDAPYARNR TAIDRVDHLD PKAMTANYPP SWRTPKWNHH GLWDWKARDV LLQTTGFFNP RRHPEWFDGG QTVADNEKTG FDVDNSENTK QGFQKEADSD KSAPIALPFE AYFANIGNLT WFGQALLVFG GNGHVTKSAH TAPLSIGVFR VRYNATGTSA TVTGWPYALL FSGMVNKQTD GLKDLPFNNN RWFEYVPRMA VAGAKFVGRE LVLAGTITMG DTATVPRLLY DELESNLNLV AQGQGLLRED LQLFTPYGWA NRPDLPIGAW SSSSSSSHNA PYYFHNNPDW QDRPIQNVVD AFIKPWEDKN GKDDAKYIYP YRYSGMWAWQ VYNWSNKLTD QPLSADFVNE NAYQPNSLFA AILNPELLAA LPDKVKYGKE NEFAANEYER FNQKLTVAPT QGTNWSHFSP TLSRFSTGFN LVGSVLDQVL DYVPWIGNGY RYGNNHRGVD DITAPRSFLP TFSNIGVGLK ANVQATLNLQ LWTGAGWRND KASSGQSDEN HTKFTSATGM DTSAGNPDSL KQDSGDSLTT QDGNAIDQQE ATNYTNLPPN LTPTADWPNA LSFTNKNNAQ RAQLFLRGLL GSIPVLVNRS GSDSNKFQAT DQKWSYTDLH SDQTKLNLPA YGEVNGLLNP ALVETYFGNT RAGGSGSNTT SSPGIGFKIP EQNNDSKATL ITPGLAWTPQ DVGNLVVSGT TVSFQLGGWL VTFTDFVKPR AGYLGLQLTG LDASDATQRA LIWAPRPWAA FRGSWVNRLG RVESVWDLKG VWADQAQSDS QGSTTTATRN ALPEHPNALA FQVSVVEASA YKPNSTNSSP YLHLVKPKKV TQSDKLDDDL KNLLDPNQVR TKLRQSFGTD HSTQPQPQSL KTTTPVFGTS SGNLSSVLSL SPVEKVSGWL VGQLPTNNLA PNTNTGNDVV GVGRLSESNA AKMNDDVDGI VRTPLAELLD GEGQTADTGP QSVKFKSPDQ IDFNRLFTHP VTDLFDPVTM LVYDQYIPLF IDIPASVNPK MVRLKVLSFD TNEQSLGLRL EFFKPDQDGD FLPLLTASSQ GPQTLFSPF

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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

BufferpH: 7.4
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy

MicroscopeJEOL CRYO ARM 300
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 2.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6rut

Final reconstructionResolution.type: BY AUTHOR / Resolution: 12.0 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES / Number images used: 9565198
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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