[English] 日本語
Yorodumi
- PDB-5nbd: PglK flippase in complex with inhibitory nanobody -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5nbd
TitlePglK flippase in complex with inhibitory nanobody
Components
  • Nanobody
  • WlaB protein
KeywordsTRANSPORT PROTEIN / ABC transporter flippase / nanobody
Function / homology
Function and homology information


ABC-type lipopolysaccharide transporter / lipopolysaccharide floppase activity / protein N-linked glycosylation via asparagine / protein N-linked glycosylation / ABC-type transporter activity / ATP hydrolysis activity / ATP binding / membrane / metal ion binding / plasma membrane
Similarity search - Function
Type 1 protein exporter / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. ...Type 1 protein exporter / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / ABC transporter ATP-binding protein / Protein glycosylation K
Similarity search - Component
Biological speciesCampylobacter jejuni (Campylobacter)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.9 Å
AuthorsPerez, C. / Pardon, E. / Steyaert, J. / Locher, K.P.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science FoundationSNF 31003AB_131075 and 310030B_166672 Switzerland
CitationJournal: Sci Rep / Year: 2017
Title: Structural basis of inhibition of lipid-linked oligosaccharide flippase PglK by a conformational nanobody.
Authors: Perez, C. / Kohler, M. / Janser, D. / Pardon, E. / Steyaert, J. / Zenobi, R. / Locher, K.P.
History
DepositionMar 1, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 3, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: WlaB protein
B: WlaB protein
C: Nanobody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,1515
Polymers142,2973
Non-polymers8542
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15300 Å2
ΔGint-118 kcal/mol
Surface area57550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.340, 142.660, 199.480
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121

-
Components

#1: Protein WlaB protein


Mass: 64587.676 Da / Num. of mol.: 2 / Mutation: E510Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni (Campylobacter) / Gene: wlaB / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O86150, UniProt: Q0P9C4*PLUS
#2: Antibody Nanobody


Mass: 13121.480 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli BL21(DE3) (bacteria)
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.22 Å3/Da / Density % sol: 70.83 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7.3 / Details: MOPS: NaCl: PEG300

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 30, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.9→29.349 Å / Num. all: 307777 / Num. obs: 42284 / % possible obs: 99.87 % / Redundancy: 13.6 % / Biso Wilson estimate: 180.94 Å2 / Rrim(I) all: 0.107 / Net I/σ(I): 13
Reflection shellResolution: 3.9→4 Å / Mean I/σ(I) obs: 1.02 / Num. measured obs: 23226 / Num. unique all: 3161 / % possible all: 99.9

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
XSCALEdata scaling
PHASERphasing
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5C78 and 4UU9

5c78

4uu9


Resolution: 3.9→29.349 Å / SU ML: 0.79 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 38.65
RfactorNum. reflection% reflection
Rfree0.335 3746 8.87 %
Rwork0.311 --
obs0.313 42249 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 292.21 Å2 / Biso mean: 163.4963 Å2 / Biso min: 89.28 Å2
Refinement stepCycle: final / Resolution: 3.9→29.349 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10037 0 38 0 10075
Biso mean--202.42 --
Num. residues----1251
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00310283
X-RAY DIFFRACTIONf_angle_d0.60713861
X-RAY DIFFRACTIONf_chiral_restr0.0381594
X-RAY DIFFRACTIONf_plane_restr0.0031709
X-RAY DIFFRACTIONf_dihedral_angle_d17.2436171
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.9-3.94930.4351440.428714391583100
3.9493-4.00110.46531400.417114261566100
4.0011-4.05580.43271400.413714251565100
4.0558-4.11360.39771370.400414071544100
4.1136-4.17480.4071440.397614601604100
4.1748-4.23990.45011440.382214391583100
4.2399-4.30920.39021350.348713941529100
4.3092-4.38320.33681350.345714071542100
4.3832-4.46270.31681450.369914701615100
4.4627-4.54820.3561340.330214011535100
4.5482-4.64070.32141390.328314321571100
4.6407-4.74120.35891390.318114281567100
4.7412-4.8510.3351380.323514091547100
4.851-4.97170.33011430.314714521595100
4.9717-5.10550.35561330.304614221555100
5.1055-5.25490.39071460.319914331579100
5.2549-5.42350.37661350.327714101545100
5.4235-5.6160.43371370.363314251562100
5.616-5.83920.35181360.35481412154899
5.8392-6.10270.42041350.369314291564100
6.1027-6.42130.38261430.369614371580100
6.4213-6.81890.38471350.361314131548100
6.8189-7.33770.31661420.332914191561100
7.3377-8.06220.2831390.294114421581100
8.0622-9.19730.24681370.245614371574100
9.1973-11.47140.25091350.20811400153599
11.4714-29.34970.3431360.3091435157199

+
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