[English] 日本語
Yorodumi
- PDB-8f6v: Crystal Structure of Nanobody VHH108 Bound to Its Antigen PA14 Cif -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8f6v
TitleCrystal Structure of Nanobody VHH108 Bound to Its Antigen PA14 Cif
Components
  • CFTR inhibitory factor
  • Nanobody VHH108
KeywordsIMMUNE SYSTEM / Pseudomonas aeruginosa / nanobody VHH / immunoglobulin domain / CFTR inhibitory factor (Cif)
Function / homologyAlpha/beta hydrolase family / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold / CFTR inhibitory factor
Function and homology information
Biological speciesVicugna pacos (alpaca)
Pseudomonas aeruginosa PA14 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsSimard, A.R. / Madden, D.R.
Funding support United States, 5items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01-AI091699 United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)P30-DK117469 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P20-GM113132 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)T32AI007519 United States
Cystic Fibrosis FoundationSTANTO19R0 United States
Citation
Journal: To Be Published
Title: Crystal Structure of Nanobody VHH113 Bound to Its Antigen PA14 Cif
Authors: Simard, A.R. / Madden, D.R.
#1: Journal: Anal Chim Acta / Year: 2019
Title: Nanobody-based binding assay for the discovery of potent inhibitors of CFTR inhibitory factor (Cif).
Authors: Vasylieva, N. / Kitamura, S. / Dong, J. / Barnych, B. / Hvorecny, K.L. / Madden, D.R. / Gee, S.J. / Wolan, D.W. / Morisseau, C. / Hammock, B.D.
#2: Journal: Acta Crystallogr D Biol Crystallogr / Year: 2012
Title: Towards automated crystallographic structure refinement with phenix.refine.
Authors: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D.
History
DepositionNov 17, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Nanobody VHH108
D: CFTR inhibitory factor
B: Nanobody VHH108
C: CFTR inhibitory factor


Theoretical massNumber of molelcules
Total (without water)96,6594
Polymers96,6594
Non-polymers00
Water4,810267
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, Cif is an obligate homodimer. The biological assembly contains one Cif dimer and two nanobody VHH108 molecules.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)98.995, 98.995, 196.987
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Space group name HallP61
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: -x,-y,z+1/2

-
Components

#1: Antibody Nanobody VHH108


Mass: 14164.782 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca) / Plasmid: pET16b / Details (production host): N-terminal 10X-His-SUMO fusion / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): DE3 RIL
#2: Protein CFTR inhibitory factor /


Mass: 34164.699 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PA14 (bacteria) / Gene: PA2394 / Plasmid: pDPM73 / Details (production host): C-terminal 6X-His / Production host: Escherichia coli (E. coli) / Strain (production host): TOP10 / References: UniProt: A0A0M3KL26
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 267 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.89 Å3/Da / Density % sol: 57.41 %
Crystal growTemperature: 292.8 K / Method: vapor diffusion / pH: 6.5
Details: Morpheus I Condition G2 (composition by Molecular Dimensions stock solutions with catalogue numbers listed at end) 20% (v/v) ethylene glycol, 10% (w/v) PEG8000, 20 mM sodium formate, 20 mM ...Details: Morpheus I Condition G2 (composition by Molecular Dimensions stock solutions with catalogue numbers listed at end) 20% (v/v) ethylene glycol, 10% (w/v) PEG8000, 20 mM sodium formate, 20 mM ammonium acetate, 20 mM sodium citrate tribasic dihydrate, 20 mM potassium sodium tartrate tetrahydrate, 20 mM sodium oxamate, 100 mM imidazole/MES monohydrate (acid) pH 6.5 Stock mixtures listed below with catalogue number in brackets. 30% (v/v) Precipitant Mix 2 [MD2-100-82], 100 mM carboxylic acids mix [MD2-100-76], 100 mM Buffer System 1 pH 6.5 [MD2-100-100]

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.979312 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 7, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979312 Å / Relative weight: 1
ReflectionResolution: 2.3→44.23 Å / Num. obs: 48028 / % possible obs: 99.26 % / Redundancy: 2.9 % / Biso Wilson estimate: 49.93 Å2 / CC1/2: 0.991 / CC star: 0.998 / Rmerge(I) obs: 0.08607 / Rpim(I) all: 0.05634 / Rrim(I) all: 0.1034 / Net I/σ(I): 7.36
Reflection shellResolution: 2.3→2.382 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.7833 / Mean I/σ(I) obs: 1.28 / Num. unique obs: 4792 / CC1/2: 0.425 / CC star: 0.772 / Rpim(I) all: 0.6205 / Rrim(I) all: 1.004 / % possible all: 99.79

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KD2, 8E1B

3kd2

8e1b


Resolution: 2.3→44.23 Å / SU ML: 0.2789 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.5748
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Details: Atoms modeled with zero occupancy could not be placed with confidence and were selected for zero-occupancy flagging after manual inspection of the 2Fo-Fc map at a 0.5-sigma cutoff.
RfactorNum. reflection% reflection
Rfree0.2098 2417 5.03 %
Rwork0.1813 45603 -
obs0.1827 48020 99.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 57.77 Å2
Refinement stepCycle: LAST / Resolution: 2.3→44.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6554 0 0 267 6821
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00916740
X-RAY DIFFRACTIONf_angle_d0.97689141
X-RAY DIFFRACTIONf_chiral_restr0.0595960
X-RAY DIFFRACTIONf_plane_restr0.0081204
X-RAY DIFFRACTIONf_dihedral_angle_d14.12382449
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.350.3461270.29062716X-RAY DIFFRACTION99.86
2.35-2.40.33951220.28512697X-RAY DIFFRACTION99.68
2.4-2.450.30591260.26632682X-RAY DIFFRACTION99.43
2.45-2.520.29382390.25532587X-RAY DIFFRACTION99.12
2.52-2.580.26351220.25092679X-RAY DIFFRACTION99.26
2.58-2.660.24211190.24322703X-RAY DIFFRACTION98.84
2.66-2.740.2591220.23412657X-RAY DIFFRACTION97.58
2.75-2.840.27521190.21562677X-RAY DIFFRACTION98.76
2.84-2.960.31091230.22212656X-RAY DIFFRACTION98.02
2.96-3.090.25462500.2192604X-RAY DIFFRACTION99.27
3.09-3.250.23381220.20342679X-RAY DIFFRACTION99.79
3.25-3.460.1991240.1982731X-RAY DIFFRACTION99.9
3.46-3.730.21771220.1742739X-RAY DIFFRACTION99.93
3.73-4.10.19361210.16272703X-RAY DIFFRACTION99.68
4.1-4.690.1561190.13152735X-RAY DIFFRACTION99.79
4.69-5.910.16962320.14272606X-RAY DIFFRACTION99.51
5.91-44.230.15991080.15252752X-RAY DIFFRACTION99.24
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)
13.293794008950.373258936276-0.09642419893262.16740285846-0.3522196818752.102816358410.0286132417895-0.0587122395740.620763131714-0.1595941608530.0108041224455-0.302707237939-0.4206950318460.473608040148-0.04480495513970.438028600785-0.05024278643670.04178513411540.467752408017-0.07724140977370.48683896984215.1284861984-21.7277140229-9.99865133698
22.400122557240.854371900735-0.101078246842.27200516645-0.8275250934481.8720666388-0.0542431725804-0.309907158390.1225868410370.2640483843560.0161797496191-0.554950717188-0.5093613902460.2874166040330.0284911177850.662834520940.006616759209780.0002129696942010.491547371628-0.1107208955850.563268177076-13.679376892322.934710120610.7185533583
31.73066921262-0.521183830168-0.3400005118311.620777607790.1216331248431.250698896180.06324899081280.057802083841-0.378583345428-0.06476048548320.007162415958990.2734315965020.21136668464-0.134930200101-0.06632029594070.397537445278-0.0228104901082-0.08804689096080.3538773818040.003351455221350.440237779514-19.1964176059-35.3218746971-7.60524300705
41.5385590412-0.3334994529140.005534983171142.142461587690.3312517771971.05120347898-0.0253228420846-0.179062950369-0.06104365169320.1904920140730.08077260045430.454490232966-0.11033244407-0.366245498521-0.05748428336980.3668969586220.05971311191240.05649416879390.4823003907410.0701192716470.389229321184-40.1209260472-2.461200925138.1645534288
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11Chain AAA4 - 1261 - 123
22Chain BBC4 - 1251 - 122
33Chain CCD26 - 3191 - 294
44Chain DDB26 - 3191 - 294

+
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