[English] 日本語
Yorodumi
- EMDB-73874: Cryo-EM structure of Protein involved in colonization (Pic) from ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-73874
TitleCryo-EM structure of Protein involved in colonization (Pic) from Enteroaggregative Escherichia coli complexed with the fragment antigen binding domain of monoclonal antibody 40
Map datasharpened map
Sample
  • Complex: Binary complex of the recombinant Pic passenger domain with Fab 40
    • Complex: Protein involved in colonization (Pic) from Enteroaggregative Escherichia coli passenger domain
      • Protein or peptide: Serine protease pic autotransporter
    • Complex: Fragment antigen binding domain of monoclonal antibody 40
      • Protein or peptide: Heavy chain of the fragment antigen binding domain of monoclonal antibody 40
      • Protein or peptide: Light chain of the fragment antigen binding domain of monoclonal antibody 40
KeywordsPROTEASE / BETA-HELIX / SECRETED / MONOCLONAL ANTIBODY / HYDROLASE / HYDROLASE-IMMUNE SYSTEM complex
Function / homology
Function and homology information


translocation of peptides or proteins into host / Secretion of toxins / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / cell outer membrane / periplasmic space / serine-type endopeptidase activity / cell surface / proteolysis / extracellular region
Similarity search - Function
: / PIC/HAP1/IgA0 second beta-solenoid repeat region / : / Peptidase S6, IgA endopeptidase / Peptidase family S6 domain / Immunoglobulin A1 protease / Peptidase family S6 domain profile. / Autotransporter beta-domain / Outer membrane autotransporter barrel / Autotransporter beta-domain ...: / PIC/HAP1/IgA0 second beta-solenoid repeat region / : / Peptidase S6, IgA endopeptidase / Peptidase family S6 domain / Immunoglobulin A1 protease / Peptidase family S6 domain profile. / Autotransporter beta-domain / Outer membrane autotransporter barrel / Autotransporter beta-domain / Autotransporter beta-domain profile. / Autotransporter beta-domain / Autotransporter beta-domain superfamily / Autotransporter, pectate lyase C-like domain superfamily / Pectin lyase fold/virulence factor
Similarity search - Domain/homology
Serine protease pic autotransporter
Similarity search - Component
Biological speciesEscherichia coli 042 (bacteria) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.69 Å
AuthorsBuckley DP / Berndsen ZT
Funding support United States, 4 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI089894 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI126887 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)T32AI007172 United States
Department of Veterans Affairs (VA, United States)5I01BX001469-05 United States
CitationJournal: To Be Published
Title: Human infection with enterotoxigenic E. coli elicits antibodies that broadly neutralize mucin-degrading proteases of pathogenic E. coli and Shigella
Authors: Buckley DP / Akhtar M / Thapa M / Schmitz A / Turner J / Vickers TJ / Khatoon N / Kaisar H / Coggin JA / Ganguli D / Sheikh A / Laird RM / Poly F / Porter CK / Ruiz-Perez F / Miller MJ / ...Authors: Buckley DP / Akhtar M / Thapa M / Schmitz A / Turner J / Vickers TJ / Khatoon N / Kaisar H / Coggin JA / Ganguli D / Sheikh A / Laird RM / Poly F / Porter CK / Ruiz-Perez F / Miller MJ / Bhuiyan TR / Qadri F / Trillo-Muyo S / Dolan B / van der Post S / Ellebedy A / Berndsen ZT / Fleckenstein JM
History
DepositionNov 16, 2025-
Header (metadata) releaseJun 3, 2026-
Map releaseJun 3, 2026-
UpdateJun 3, 2026-
Current statusJun 3, 2026Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_73874.png

Downloads & links

-
Map

FileDownload / File: emd_73874.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.94 Å/pix.
x 320 pix.
= 300.16 Å		0.94 Å/pix.
x 320 pix.
= 300.16 Å		0.94 Å/pix.
x 320 pix.
= 300.16 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.938 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.122
Minimum - Maximum-0.45835525 - 0.7062506
Average (Standard dev.)0.000018347953 (±0.01709659)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 300.16 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: half map A

Fileemd_73874_half_map_1.map
Annotationhalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half map B

Fileemd_73874_half_map_2.map
Annotationhalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Binary complex of the recombinant Pic passenger domain with Fab 40

EntireName: Binary complex of the recombinant Pic passenger domain with Fab 40
Components
  • Complex: Binary complex of the recombinant Pic passenger domain with Fab 40
    • Complex: Protein involved in colonization (Pic) from Enteroaggregative Escherichia coli passenger domain
      • Protein or peptide: Serine protease pic autotransporter
    • Complex: Fragment antigen binding domain of monoclonal antibody 40
      • Protein or peptide: Heavy chain of the fragment antigen binding domain of monoclonal antibody 40
      • Protein or peptide: Light chain of the fragment antigen binding domain of monoclonal antibody 40

-
Supramolecule #1: Binary complex of the recombinant Pic passenger domain with Fab 40

SupramoleculeName: Binary complex of the recombinant Pic passenger domain with Fab 40
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli 042 (bacteria)
Molecular weightTheoretical: 23 KDa

-
Supramolecule #2: Protein involved in colonization (Pic) from Enteroaggregative Esc...

SupramoleculeName: Protein involved in colonization (Pic) from Enteroaggregative Escherichia coli passenger domain
type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Details: Mature, secreted Pic passenger domain (cleaved N-terminal signal peptide and C-terminal beta-barrel regions) from recombinant expression of full-length Pic
Source (natural)Organism: Escherichia coli 042 (bacteria)

-
Supramolecule #3: Fragment antigen binding domain of monoclonal antibody 40

SupramoleculeName: Fragment antigen binding domain of monoclonal antibody 40
type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3
Details: Fab fragment generated from papain-digested monoclonal 40 IgG
Source (natural)Organism: Homo sapiens (human)

-
Macromolecule #1: Serine protease pic autotransporter

MacromoleculeName: Serine protease pic autotransporter / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
EC number: Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
Source (natural)Organism: Escherichia coli 042 (bacteria)
Molecular weightTheoretical: 109.896367 KDa
Recombinant expressionOrganism: Escherichia coli 042 (bacteria)
SequenceString: GIVRSDIAYQ IYRDFAENKG LFVPGANDIP VYDKDGKLVG RLGKAPMADF SSVSSNGVAT LVSPQYIVSV KHNGGYRSVS FGNGKNTYS LVDRNNHPSI DFHAPRLNKL VTEVIPSAVT SEGTKANAYK YTERYTAFYR VGSGTQYTKD KDGNLVKVAG G YAFKTGGT ...String:
GIVRSDIAYQ IYRDFAENKG LFVPGANDIP VYDKDGKLVG RLGKAPMADF SSVSSNGVAT LVSPQYIVSV KHNGGYRSVS FGNGKNTYS LVDRNNHPSI DFHAPRLNKL VTEVIPSAVT SEGTKANAYK YTERYTAFYR VGSGTQYTKD KDGNLVKVAG G YAFKTGGT TGVPLISDAT IVSNPGQTYN PVNGPLPDYG APGDSGSPLF AYDKQQKKWV IVAVLRAYAG INGATNWWNV IP TDYLNQV MQDDFDAPVD FVSGLGPLNW TYDKTSGTGT LSQGSKNWTM HGQKDNDLNA GKNLVFSGQN GAIILKDSVT QGA GYLEFK DSYTVSAESG KTWTGAGIIT DKGTNVTWKV NGVAGDNLHK LGEGTLTING TGVNPGGLKT GDGIVVLNQQ ADTA GNIQA FSSVNLASGR PTVVLGDARQ VNPDNISWGY RGGKLDLNGN AVTFTRLQAA DYGAVITNNA QQKSQLLLDL KAQDT NVSE PTIGNISPFG GTGTPGNLYS MILNSQTRFY ILKSASYGNT LWGNSLNDPA QWEFVGMDKN KAVQTVKDRI LAGRAK QPV IFHGQLTGNM DVAIPQVPGG RKVIFDGSVN LPEGTLSQDS GTLIFQGHPV IHASISGSAP VSLNQKDWEN RQFTMKT LS LKDADFHLSR NASLNSDIKS DNSHITLGSD RAFVDKNDGT GNYVIPEEGT SVPDTVNDRS QYEGNITLNH NSALDIGS R FTGGIDAYDS AVSITSPDVL LTAPGAFAGS SLTVHDGGHL TALNGLFSDG HIQAGKNGKI TLSGTPVKDT ANQYAPAVY LTDGYDLTGD NAALEITRGA HASGDIHASA ASTVTIGSDT PAELASAETA ASAFAGSLLE GYNAAFNGAI TGGRADVSMH NALWTLGGD SAIHSLTVRN SRISSEGDRT FRTLTVNKLD ATGSDFVLRT DLKNADKINV TEKATGSDNS LNVSFMNNPA Q GQALNIPL VTAPAGTSAE MFKAGTRVTG FSRVTPTLHV DTSGGNTKWI LDGFKAEADK AAAAKADSFM NAGYKNFMTE VN

UniProtKB: Serine protease pic autotransporter

-
Macromolecule #2: Heavy chain of the fragment antigen binding domain of monoclonal ...

MacromoleculeName: Heavy chain of the fragment antigen binding domain of monoclonal antibody 40
type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.757502 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVQLQESGPG LVKPSETLSL TCTVSGASIS SSSYYCIWVR QSPGKGLEWI GTTYYSGTTY HEPSLRSRVS ISLDTSKNQF SLMLTSVTA ADTARYYCAI SYGWGSYVNH WGQGTLVTVS SASTKGPSVF PLAPSSKSTS GGTAALGCLV KDYFPEPVTV S WNSGALTS ...String:
QVQLQESGPG LVKPSETLSL TCTVSGASIS SSSYYCIWVR QSPGKGLEWI GTTYYSGTTY HEPSLRSRVS ISLDTSKNQF SLMLTSVTA ADTARYYCAI SYGWGSYVNH WGQGTLVTVS SASTKGPSVF PLAPSSKSTS GGTAALGCLV KDYFPEPVTV S WNSGALTS GVHTFPAVLQ SSGLYSLSSV VTVPSSSLGT QTYICNVNHK PSNTKVDKRV EPKSCD

-
Macromolecule #3: Light chain of the fragment antigen binding domain of monoclonal ...

MacromoleculeName: Light chain of the fragment antigen binding domain of monoclonal antibody 40
type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.534123 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EIVLTQSPAT LSLSPGERAT LSCRASQIFG SDLAWYQHKP GQAPRLLIFN TSNRVTGTPA RFSGSGSGTD FTLTINSLEP DDVAVYYCH QRSSWPSITF GQGTRLEIKR TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD ...String:
EIVLTQSPAT LSLSPGERAT LSCRASQIFG SDLAWYQHKP GQAPRLLIFN TSNRVTGTPA RFSGSGSGTD FTLTINSLEP DDVAVYYCH QRSSWPSITF GQGTRLEIKR TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD SKDSTYSLSS TLTLSKADYE KHKVYACEVT HQGLSSPVTK SFNRGEC

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.2 mg/mL
BufferpH: 7.4 / Component - Concentration: 1.0 X / Component - Formula: TBS / Component - Name: Tris-Buffered Saline
Details: 10X TBS: 250mM Tris, 27mM potassium chloride, 1.37M sodium chloride, pH 7.4
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Support film - Film thickness: 50 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 15 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.039 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV
Details: Added 1X Lauryl Maltose Neopentyl Glycol (LMNG) detergent to sample prior to vitrification..
DetailsThis sample displayed heterogeneity in the ice, resulting in preferred orientation in the final map.

-
Electron microscopy

MicroscopeTFS KRIOS
TemperatureMin: 87.15 K / Max: 87.15 K
Specialist opticsEnergy filter - Name: TFS Selectris / Energy filter - Slit width: 10 eV
SoftwareName: EPU / Details: TFS EPU
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Number grids imaged: 1 / Number real images: 2917 / Average exposure time: 3.78 sec. / Average electron dose: 41.0 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: 2.2 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 130000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 1071006
Details: Initial particle set was obtained by CryoSegNet AI picking, followed by cryoSPARC 2D classification to redo particle picking with 2D templates
CTF correctionSoftware - Name: cryoSPARC (ver. 4.7.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: AB-INITIO
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.69 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7.1) / Number images used: 127391
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.7.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.7.1)
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
SoftwareName: UCSF ChimeraX (ver. 1.8)
DetailsRigid body fitting of AlphaFold-derived models was done in ChimeraX, followed by multiple rounds of local fitting in Coot and Phenix real-space refinement
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Target criteria: Cross-correlation coefficient
Output model

PDB-9z7b:
Cryo-EM structure of Protein involved in colonization (Pic) from Enteroaggregative Escherichia coli complexed with the fragment antigen binding domain of monoclonal antibody 40

+
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