[English] 日本語
Yorodumi
- PDB-7omt: Crystal structure of ProMacrobody 21 with bound maltose -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7omt
TitleCrystal structure of ProMacrobody 21 with bound maltose
ComponentsProMacrobody 21
KeywordsIMMUNE SYSTEM / nanobody Cryo-EM Chaperone MBP
Function / homologyalpha-maltose
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsBotte, M. / Ni, D. / Schenck, S. / Zimmermann, I. / Chami, M. / Bocquet, N. / Egloff, P. / Bucher, D. / Trabuco, M. / Cheng, R.K.Y. ...Botte, M. / Ni, D. / Schenck, S. / Zimmermann, I. / Chami, M. / Bocquet, N. / Egloff, P. / Bucher, D. / Trabuco, M. / Cheng, R.K.Y. / Brunner, J.D. / Seeger, M.A. / Stahlberg, H. / Hennig, M.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Innosuisse25864.1 PFLS-LS Switzerland
CitationJournal: Nat Commun / Year: 2022
Title: Cryo-EM structures of a LptDE transporter in complex with Pro-macrobodies offer insight into lipopolysaccharide translocation.
Authors: Mathieu Botte / Dongchun Ni / Stephan Schenck / Iwan Zimmermann / Mohamed Chami / Nicolas Bocquet / Pascal Egloff / Denis Bucher / Matilde Trabuco / Robert K Y Cheng / Janine D Brunner / ...Authors: Mathieu Botte / Dongchun Ni / Stephan Schenck / Iwan Zimmermann / Mohamed Chami / Nicolas Bocquet / Pascal Egloff / Denis Bucher / Matilde Trabuco / Robert K Y Cheng / Janine D Brunner / Markus A Seeger / Henning Stahlberg / Michael Hennig /
Abstract: Lipopolysaccharides are major constituents of the extracellular leaflet in the bacterial outer membrane and form an effective physical barrier for environmental threats and for antibiotics in Gram- ...Lipopolysaccharides are major constituents of the extracellular leaflet in the bacterial outer membrane and form an effective physical barrier for environmental threats and for antibiotics in Gram-negative bacteria. The last step of LPS insertion via the Lpt pathway is mediated by the LptD/E protein complex. Detailed insights into the architecture of LptDE transporter complexes have been derived from X-ray crystallography. However, no structure of a laterally open LptD transporter, a transient state that occurs during LPS release, is available to date. Here, we report a cryo-EM structure of a partially opened LptDE transporter in complex with rigid chaperones derived from nanobodies, at 3.4 Å resolution. In addition, a subset of particles allows to model a structure of a laterally fully opened LptDE complex. Our work offers insights into the mechanism of LPS insertion, provides a structural framework for the development of antibiotics targeting LptD and describes a highly rigid chaperone scaffold to enable structural biology of challenging protein targets.
History
DepositionMay 24, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 4, 2022Provider: repository / Type: Initial release
Revision 1.1May 11, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ProMacrobody 21
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,6465
Polymers56,7141
Non-polymers9314
Water2,756153
1
A: ProMacrobody 21
hetero molecules

A: ProMacrobody 21
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,29110
Polymers113,4292
Non-polymers1,8638
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,y,-z1
Buried area5110 Å2
ΔGint-10 kcal/mol
Surface area41740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.897, 87.624, 118.635
Angle α, β, γ (deg.)90.000, 99.076, 90.000
Int Tables number5
Space group name H-MI121
Space group name HallC2y(x,y,-x+z)
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z+1/2
#4: -x+1/2,y+1/2,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-763-

HOH

21A-841-

HOH

31A-844-

HOH

41A-848-

HOH

-
Components

#1: Antibody ProMacrobody 21


Mass: 56714.457 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.35 Å3/Da / Density % sol: 47.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: in 0.2 M MgCl2, 0.1M Hepes pH 7.5, 30% PEG400

-
Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Sep 30, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→44.45 Å / Num. obs: 34750 / % possible obs: 98.1 % / Redundancy: 7.1 % / Biso Wilson estimate: 43.84 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.057 / Net I/σ(I): 15.1
Reflection shellResolution: 2→2.05 Å / Rmerge(I) obs: 1.167 / Num. unique obs: 34750 / CC1/2: 0.722

-
Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
PHENIX1.16_3549refinement
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1N3W, 5FWO

1n3w

5fwo


Resolution: 2→44.45 Å / SU ML: 0.2398 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.0245
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2394 1700 4.89 %
Rwork0.1929 33037 -
obs0.1951 34737 97.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 62.19 Å2
Refinement stepCycle: LAST / Resolution: 2→44.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3757 0 48 153 3958
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013913
X-RAY DIFFRACTIONf_angle_d1.02065318
X-RAY DIFFRACTIONf_chiral_restr0.0607570
X-RAY DIFFRACTIONf_plane_restr0.0067685
X-RAY DIFFRACTIONf_dihedral_angle_d12.15232305
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.060.33921310.30172689X-RAY DIFFRACTION96.58
2.06-2.130.30521480.27732717X-RAY DIFFRACTION96.95
2.13-2.20.31391420.2532720X-RAY DIFFRACTION97.12
2.2-2.290.29451510.25082679X-RAY DIFFRACTION97.22
2.29-2.390.27991380.22062750X-RAY DIFFRACTION97.6
2.39-2.520.30981350.22792752X-RAY DIFFRACTION97.93
2.52-2.680.25211390.22292753X-RAY DIFFRACTION98.07
2.68-2.880.26091590.22222762X-RAY DIFFRACTION97.99
2.88-3.170.24451450.22362738X-RAY DIFFRACTION98.7
3.17-3.630.29491320.19652802X-RAY DIFFRACTION98.79
3.63-4.580.20141560.15772796X-RAY DIFFRACTION99.06
4.58-44.450.19121240.16282879X-RAY DIFFRACTION99.21
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.447417551681.94219888408-1.696169332713.12868694131-0.8234888844774.0602782357-0.323908130680.0528890309458-0.5554421698450.1330213030720.209270179371-0.07788299447680.630208627984-0.6176254079150.02600524847010.398443383074-0.03464543622850.1306407965460.3737168912750.04024170151290.411493508745-41.2374384881-30.44711686017.08798163175
22.501142403841.30746185024-0.1470412390223.40108194545-1.163671176712.0366983588-0.3829913049460.3808332015370.359632420093-0.2125902483950.308549918991-0.089678202232-0.5210709262320.06725616137690.04175201803550.537962150961-0.1174899304720.001434467386830.4034346528820.0644035546480.366633870614-21.149080984210.6053391623-17.6253539861
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 122 )
2X-RAY DIFFRACTION2chain 'A' and (resid 123 through 482 )

+
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