[English] 日本語
Yorodumi
- EMDB-71842: Antibody fragment from mAb824 bound to the adhesin protein FimH. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-71842
TitleAntibody fragment from mAb824 bound to the adhesin protein FimH.
Map dataAntibody fragment from mAb824 bound to the E. coli adhesin protein FimH
Sample
  • Complex: Antibody fragment from mAb824 bound to the E. coli adhesin protein FimH
    • Complex: Fimbrial tip
      • Protein or peptide: Type 1 fimbrin D-mannose specific adhesin
      • Protein or peptide: Protein FimG
    • Complex: Antibody Fragments
      • Protein or peptide: mAb824 Heavy Chain
      • Protein or peptide: mAb824 Light Chain
KeywordsFimbrial tip / Lectin domain / Antibody fragments / Antibody-target complex / CELL ADHESION / CELL ADHESION-IMMUNE SYSTEM complex
Function / homology
Function and homology information


pilus tip / mechanosensory behavior / cell adhesion involved in single-species biofilm formation / pilus / cell-substrate adhesion / D-mannose binding / host cell membrane / cell adhesion
Similarity search - Function
FimH, mannose-binding domain / FimH, mannose binding / Fimbrial-type adhesion domain / Fimbrial protein / : / Fimbrial-type adhesion domain superfamily / Adhesion domain superfamily
Similarity search - Domain/homology
Protein FimG / Type 1 fimbrin D-mannose specific adhesin
Similarity search - Component
Biological speciesEscherichia coli (E. coli) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsHvorecny KL / Magala P / Klevit RE / Kollman JM
Funding support United States, 4 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM149542 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)F32 AI145111 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI171570 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)K99 GM141364 United States
CitationJournal: To Be Published
Title: Antibodies disrupt bacterial adhesion by ligand mimicry and allostery
Authors: Hvorecny KL / Kollman JM
History
DepositionJul 29, 2025-
Header (metadata) releaseNov 26, 2025-
Map releaseNov 26, 2025-
UpdateNov 26, 2025-
Current statusNov 26, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_71842.png

Downloads & links

-
Map

FileDownload / File: emd_71842.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAntibody fragment from mAb824 bound to the E. coli adhesin protein FimH
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.12 Å/pix.
x 480 pix.
= 539.52 Å		1.12 Å/pix.
x 480 pix.
= 539.52 Å		1.12 Å/pix.
x 480 pix.
= 539.52 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.124 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.0
Minimum - Maximum-17.744375000000002 - 24.643034
Average (Standard dev.)0.000001257659 (±0.13140038)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 539.51996 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: Antibody fragment from mAb824 bound to the E....

Fileemd_71842_additional_1.map
AnnotationAntibody fragment from mAb824 bound to the E. coli adhesin protein FimH masked around variable regions and FimH lectin domain
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Half map of antibody fragment from mAb824 bound...

Fileemd_71842_additional_2.map
AnnotationHalf map of antibody fragment from mAb824 bound to the E. coli adhesin protein FimH masked around variable regions and FimH lectin domain
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Half map of antibody fragment from mAb824 bound...

Fileemd_71842_additional_3.map
AnnotationHalf map of antibody fragment from mAb824 bound to the E. coli adhesin protein FimH masked around variable regions and FimH lectin domain
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map of antibody fragment from mAb824 bound...

Fileemd_71842_half_map_1.map
AnnotationHalf map of antibody fragment from mAb824 bound to the E. coli adhesin protein FimH
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map of antibody fragment from mAb824 bound...

Fileemd_71842_half_map_2.map
AnnotationHalf map of antibody fragment from mAb824 bound to the E. coli adhesin protein FimH
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Antibody fragment from mAb824 bound to the E. coli adhesin protei...

EntireName: Antibody fragment from mAb824 bound to the E. coli adhesin protein FimH
Components
  • Complex: Antibody fragment from mAb824 bound to the E. coli adhesin protein FimH
    • Complex: Fimbrial tip
      • Protein or peptide: Type 1 fimbrin D-mannose specific adhesin
      • Protein or peptide: Protein FimG
    • Complex: Antibody Fragments
      • Protein or peptide: mAb824 Heavy Chain
      • Protein or peptide: mAb824 Light Chain

-
Supramolecule #1: Antibody fragment from mAb824 bound to the E. coli adhesin protei...

SupramoleculeName: Antibody fragment from mAb824 bound to the E. coli adhesin protein FimH
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

-
Supramolecule #2: Fimbrial tip

SupramoleculeName: Fimbrial tip / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Escherichia coli (E. coli)

-
Supramolecule #3: Antibody Fragments

SupramoleculeName: Antibody Fragments / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3-#4
Source (natural)Organism: Mus musculus (house mouse) / Tissue: B cell hybridoma

-
Macromolecule #1: Type 1 fimbrin D-mannose specific adhesin

MacromoleculeName: Type 1 fimbrin D-mannose specific adhesin / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 31.48826 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKRVITLFAV LLMGWSVNAW SFACKTANGT AIPIGGGSAN VYVNLAPVVN VGQNLVVDLS TQIFCHNDYP ETITDYVTLQ RGSAYGGVL SNFSGTVKYS GSSYPFPTTS ETPRVVYNSR TDKPWPVALY LTPVSSAGGV AIKAGSLIAV LILRQTNNYN S DDFQFVWN ...String:
MKRVITLFAV LLMGWSVNAW SFACKTANGT AIPIGGGSAN VYVNLAPVVN VGQNLVVDLS TQIFCHNDYP ETITDYVTLQ RGSAYGGVL SNFSGTVKYS GSSYPFPTTS ETPRVVYNSR TDKPWPVALY LTPVSSAGGV AIKAGSLIAV LILRQTNNYN S DDFQFVWN IYANNDVVVP TGGCDVSARD VTVTLPDYPG SVPIPLTVYC AKSQNLGYYL SGTTADAGNS IFTNTASFSP AQ GVGVQLT RNGTIIPANN TVSLGAVGTS AVSLGLTANY ARTGGQVTAG NVQSIIGVTF VYQ

UniProtKB: Type 1 fimbrin D-mannose specific adhesin

-
Macromolecule #2: Protein FimG

MacromoleculeName: Protein FimG / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 17.328258 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MKWCKRGYVL AAILALASAT IQAADVTITV NGKVVAKPCT VSTTNATVDL GDLYSFSLMS AGAASAWHDV ALELTNCPVG TSRVTASFS GAADSTGYYK NQGTAQNIQL ELQDDSGNTL NTGATKTVQV DDSSQSAHFP LQVRALTVNG GATQGTIQAV I SITYTYS

UniProtKB: Protein FimG

-
Macromolecule #3: mAb824 Heavy Chain

MacromoleculeName: mAb824 Heavy Chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 22.526971 KDa
SequenceString: EIQLQQSGPE RMKPGASVKI SCKASGYSFT TYYIHWVKQS HGRSLEWIGY IDPFNDDTNY NQKFKGKATL TVDKSSSTAY MHLSSLTSE DSAVYYCARS YYGSLDYWGQ GTTLTVSSAK TTPPSVYPLA PGSAAQTNSM VTLGCLVKGY FPEPVTVTWN S GSLSSGVH ...String:
EIQLQQSGPE RMKPGASVKI SCKASGYSFT TYYIHWVKQS HGRSLEWIGY IDPFNDDTNY NQKFKGKATL TVDKSSSTAY MHLSSLTSE DSAVYYCARS YYGSLDYWGQ GTTLTVSSAK TTPPSVYPLA PGSAAQTNSM VTLGCLVKGY FPEPVTVTWN S GSLSSGVH TFPAVLQSDL YTLSSSVTVP SSTWPSETVT CNVAHPASST

-
Macromolecule #4: mAb824 Light Chain

MacromoleculeName: mAb824 Light Chain / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 21.757852 KDa
SequenceString: DIQMTQTTSS LSASLGDRVT ISCRASQGVN NYLNWYQQKP DGSVKLLIYY TSNLHSGAPS RFSGSGSGTD YSLTISNLEQ EDIATYFCQ QANMVPWTFG GGTKLEIKRA DAAPTVSIFP PSSEQLTSGG ASVVCFLNNF YPKDINVKWK IDGSERQNGV L NSWTDQDS ...String:
DIQMTQTTSS LSASLGDRVT ISCRASQGVN NYLNWYQQKP DGSVKLLIYY TSNLHSGAPS RFSGSGSGTD YSLTISNLEQ EDIATYFCQ QANMVPWTFG GGTKLEIKRA DAAPTVSIFP PSSEQLTSGG ASVVCFLNNF YPKDINVKWK IDGSERQNGV L NSWTDQDS KDSTYSMSST LTLTKDEYER HNSYTCEAR

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
GridModel: C-flat-2/1 / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING
VitrificationCryogen name: ETHANE / Instrument: HOMEMADE PLUNGER

-
Electron microscopy

MicroscopeTFS KRIOS
SoftwareName: SerialEM (ver. 4.1)
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 10383 / Average electron dose: 42.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.75 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. 4.5.3) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionAlgorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: PHENIX (ver. 1.21.1-5286) / Number images used: 306269
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.5.3)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 5.0)
Final 3D classificationNumber classes: 1

-
Atomic model buiding 1

Initial modelPDB ID:

9me5


Chain - Source name: PDB / Chain - Initial model type: experimental model
SoftwareName: UCSF ChimeraX (ver. 1.9)
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-9ptm:
Antibody fragment from mAb824 bound to the adhesin protein FimH.

+
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