[English] 日本語
Yorodumi
- PDB-4ckd: Model of complex between the E.coli enzyme beta-galactosidase and... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4ckd
TitleModel of complex between the E.coli enzyme beta-galactosidase and four single chain Fv antibody domains scFv13R4.
Components
  • BETA-GALACTOSIDASE
  • SCFV13R4 ANTIBODY FV HEAVY CHAIN
  • SCFV13R4 ANTIBODY FV LIGHT CHAIN
KeywordsHYDROLASE/IMMUNE SYSTEM / HYDROLASE-IMMUNE SYSTEM COMPLEX
Function / homology
Function and homology information


alkali metal ion binding / lactose catabolic process / beta-galactosidase complex / beta-galactosidase / beta-galactosidase activity / immunoglobulin complex / immunoglobulin mediated immune response / antigen binding / carbohydrate binding / adaptive immune response ...alkali metal ion binding / lactose catabolic process / beta-galactosidase complex / beta-galactosidase / beta-galactosidase activity / immunoglobulin complex / immunoglobulin mediated immune response / antigen binding / carbohydrate binding / adaptive immune response / immune response / magnesium ion binding / extracellular space / identical protein binding
Similarity search - Function
Glycoside hydrolase, family 2, beta-galactosidase / Beta galactosidase small chain/ domain 5 / Beta-galactosidase, domain 4 / Beta galactosidase small chain / Beta-galactosidase, domain 4 / Beta galactosidase small chain / Glycoside hydrolase, family 2, active site / Glycosyl hydrolases family 2 acid/base catalyst. / Glycoside hydrolase, family 2, conserved site / Glycosyl hydrolases family 2 signature 1. ...Glycoside hydrolase, family 2, beta-galactosidase / Beta galactosidase small chain/ domain 5 / Beta-galactosidase, domain 4 / Beta galactosidase small chain / Beta-galactosidase, domain 4 / Beta galactosidase small chain / Glycoside hydrolase, family 2, active site / Glycosyl hydrolases family 2 acid/base catalyst. / Glycoside hydrolase, family 2, conserved site / Glycosyl hydrolases family 2 signature 1. / Glycoside hydrolase, family 2 / Glycoside hydrolase family 2, catalytic domain / Glycosyl hydrolases family 2, TIM barrel domain / Glycoside hydrolase, family 2, immunoglobulin-like beta-sandwich / Glycosyl hydrolases family 2, sugar binding domain / Glycosyl hydrolases family 2 / Glycosyl hydrolases family 2, sugar binding domain / Beta-Galactosidase/glucuronidase domain superfamily / Glycoside hydrolase-type carbohydrate-binding / Galactose mutarotase-like domain superfamily / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-Type / Galactose-binding-like domain superfamily / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Glycoside hydrolase superfamily / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Beta-galactosidase / Ig kappa chain V-V region L7 / Ig heavy chain V region 36-60
Similarity search - Component
Biological speciesESCHERICHIA COLI K-12 (bacteria)
MUS MUSCULUS (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 13 Å
AuthorsVinothkumar, K.R. / McMullan, G. / Henderson, R.
CitationJournal: Structure / Year: 2014
Title: Molecular mechanism of antibody-mediated activation of β-galactosidase.
Authors: Kutti R Vinothkumar / Greg McMullan / Richard Henderson /
Abstract: Binding of a single-chain Fv antibody to Escherichia coli β-galactosidase (β-gal) is known to stabilize the enzyme and activate several inactive point mutants, historically called antibody-mediated ...Binding of a single-chain Fv antibody to Escherichia coli β-galactosidase (β-gal) is known to stabilize the enzyme and activate several inactive point mutants, historically called antibody-mediated enzyme formation mutants. To understand the nature of this activation, we have determined by electron cryo-microscopy the structure of the complex between β-gal and the antibody scFv13R4. Our structure localizes the scFv13R4 binding site to the crevice between domains 1 and 3 in each β-gal subunit. The mutations that scFv13R4 counteracts are located between the antibody binding site and the active site of β-gal, at one end of the TIM-barrel that forms domain 3 where the substrate lactose is hydrolyzed. The mode of binding suggests how scFv stabilizes both the active site of β-gal and the tetrameric state.
History
DepositionJan 3, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 15, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 26, 2014Group: Database references / Source and taxonomy / Structure summary
Revision 1.2Apr 23, 2014Group: Database references
Revision 1.3Aug 30, 2017Group: Data collection / Category: em_software
Item: _em_software.fitting_id / _em_software.image_processing_id / _em_software.name
Revision 1.4Oct 23, 2019Group: Data collection / Other / Category: cell / Item: _cell.Z_PDB

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-2548
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: BETA-GALACTOSIDASE
B: BETA-GALACTOSIDASE
C: BETA-GALACTOSIDASE
D: BETA-GALACTOSIDASE
H: SCFV13R4 ANTIBODY FV HEAVY CHAIN
I: SCFV13R4 ANTIBODY FV HEAVY CHAIN
J: SCFV13R4 ANTIBODY FV HEAVY CHAIN
K: SCFV13R4 ANTIBODY FV HEAVY CHAIN
L: SCFV13R4 ANTIBODY FV LIGHT CHAIN
M: SCFV13R4 ANTIBODY FV LIGHT CHAIN
N: SCFV13R4 ANTIBODY FV LIGHT CHAIN
O: SCFV13R4 ANTIBODY FV LIGHT CHAIN


Theoretical massNumber of molelcules
Total (without water)564,09312
Polymers564,09312
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS

-
Components

#1: Protein
BETA-GALACTOSIDASE / / BETA-GAL / LACTASE


Mass: 116602.484 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI K-12 (bacteria) / Description: SIGMA CATALOGUE NUMBER G3153 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P00722, beta-galactosidase
#2: Antibody
SCFV13R4 ANTIBODY FV HEAVY CHAIN


Mass: 12795.939 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PM12 PLYSS / References: UniProt: P01823*PLUS
#3: Antibody
SCFV13R4 ANTIBODY FV LIGHT CHAIN


Mass: 11624.795 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PM12 PLYSS / References: UniProt: P01642*PLUS
Sequence detailsTHE DEPOSITED BETA-GALACTOSIDASE SEQUENCE CONTAINS RESIDUES 4-1024 IN THE FULL GENE SEQUENCE ...THE DEPOSITED BETA-GALACTOSIDASE SEQUENCE CONTAINS RESIDUES 4-1024 IN THE FULL GENE SEQUENCE INCLUDING METHIONINE INITIATION CODON. THESE ARE NUMBERED FROM 3 TO 1023 IN THE DEPOSITION, FOLLOWING NORMAL PRACTICE FOR X- RAY DEPOSITIONS.

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: SINGLE CHAIN FV ANTIBODY DOMAIN BOUND TO THE ENZYME BETA-GALACTOSIDASE
Type: COMPLEX / Details: 49 BEST IMAGES SELECTED OUT OF 52 RECORDED
Buffer solutionName: 20% PHOSPHATE BUFFERED SALINE (PBS) / pH: 7.4 / Details: 20% PHOSPHATE BUFFERED SALINE (PBS)
SpecimenConc.: 0.9 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: HOLEY CARBON
VitrificationCryogen name: ETHANE
Details: VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 100, TEMPERATURE- 100, INSTRUMENT- OTHER, METHOD- BLOT FOR 10-20 SECONDS UNTIL DIAMETER OF BLOTTED MENISCUS CEASES TO EXPAND, BEFORE PLUNGING.

-
Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyModel: FEI POLARA 300 / Date: Aug 2, 2012
Details: EXPOSURE INTENSITY SET TO GIVE 50 ELECTRONS PER PIXEL PER SECOND AT THE DETECTOR. THIS TRANSLATES INTO 16 ELECTRONS PER SQUARE ANGSTROM PER SECOND AT THE SPECIMEN.
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 59000 X / Calibrated magnification: 81600 X / Nominal defocus max: 4027 nm / Nominal defocus min: 2678 nm / Cs: 2 mm
Specimen holderTemperature: 89 K
Image recordingElectron dose: 67 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)
Image scansNum. digital images: 49
Radiation wavelengthRelative weight: 1

-
Processing

EM software
IDNameVersionCategory
1CTFFIND3CTF correction
2UCSF Chimeramodel fitting
3FREALIGN3D reconstruction
4MRC IMAGE PROCESSING PACKAGE3D reconstruction
CTF correctionDetails: DONE INSIDE FREALIGN
SymmetryPoint symmetry: D2 (2x2 fold dihedral)
3D reconstructionMethod: PROJECTION MATCHING / Resolution: 13 Å / Num. of particles: 2965 / Nominal pixel size: 1.74 Å / Actual pixel size: 1.72 Å
Magnification calibration: MAGNIFICATION REFINED BY MAXIMISING FSC AGAINST ATOMIC MODEL
Details: FREALIGN MAP OBTAINED FROM 2965 PARTICLES USING D2 SYMMETRY THIS IS A MODEL MADE BY DOCKING TWO ATOMIC MODELS AS RIGID BODIES INTO A 13 ANGSTROM RESOLUTION DENSITY MAP. SUBMISSION BASED ON ...Details: FREALIGN MAP OBTAINED FROM 2965 PARTICLES USING D2 SYMMETRY THIS IS A MODEL MADE BY DOCKING TWO ATOMIC MODELS AS RIGID BODIES INTO A 13 ANGSTROM RESOLUTION DENSITY MAP. SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2548. (DEPOSITION ID: 12230).
Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL / Target criteria: FSC CURVE BETWEEN MAP AND MODEL / Details: METHOD--RIGID BODY REFINEMENT PROTOCOL--X-RAY
Atomic model buildingPDB-ID: 1F4A

1f4a

RefinementHighest resolution: 13 Å
Refinement stepCycle: LAST / Highest resolution: 13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms39672 0 0 0 39672

+
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