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- PDB-6avz: Crystal structure of the HopQ-CEACAM3 WT complex -

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Basic information

Entry
Database: PDB / ID: 6avz
TitleCrystal structure of the HopQ-CEACAM3 WT complex
Components
  • Carcinoembryonic antigen-related cell adhesion molecule 3
  • HopQ
  • part of HopQ loop
KeywordsCELL ADHESION
Function / homology
Function and homology information


regulation of immune system process / specific granule membrane / protein tyrosine kinase binding / Cell surface interactions at the vascular wall / Neutrophil degranulation / cell surface / signal transduction / plasma membrane
Similarity search - Function
: / SabA, N-terminal extracellular adhesion domain / SabA N-terminal extracellular adhesion domain / Outer membrane protein, Helicobacter / Helicobacter outer membrane protein / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins ...: / SabA, N-terminal extracellular adhesion domain / SabA N-terminal extracellular adhesion domain / Outer membrane protein, Helicobacter / Helicobacter outer membrane protein / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
HopQ / Cell adhesion molecule CEACAM3
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
Homo sapiens (human)
Helicobacter pylori P12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsBonsor, D.A. / Sundberg, E.J.
CitationJournal: EMBO J. / Year: 2018
Title: TheHelicobacter pyloriadhesin protein HopQ exploits the dimer interface of human CEACAMs to facilitate translocation of the oncoprotein CagA.
Authors: Bonsor, D.A. / Zhao, Q. / Schmidinger, B. / Weiss, E. / Wang, J. / Deredge, D. / Beadenkopf, R. / Dow, B. / Fischer, W. / Beckett, D. / Wintrode, P.L. / Haas, R. / Sundberg, E.J.
History
DepositionSep 5, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 11, 2018Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: HopQ
A: Carcinoembryonic antigen-related cell adhesion molecule 3
E: part of HopQ loop
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,4275
Polymers59,3473
Non-polymers802
Water1,13563
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2410 Å2
ΔGint-31 kcal/mol
Surface area20990 Å2
Unit cell
Length a, b, c (Å)39.479, 103.263, 112.565
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number17
Space group name H-MP2221
Components on special symmetry positions
IDModelComponents
11B-502-

CA

21A-216-

HOH

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Components

#1: Protein HopQ


Mass: 47027.602 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Gene: hopQ / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: H6A3H4
#2: Protein Carcinoembryonic antigen-related cell adhesion molecule 3 / Carcinoembryonic antigen CGM1


Mass: 12045.568 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CEACAM3, CD66D, CGM1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P40198
#3: Protein/peptide part of HopQ loop


Mass: 273.330 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori P12 (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 1.94 Å3/Da / Density % sol: 36.51 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 20% w/v PEG 3000, 0.1 M Bis-Tris-HCl, pH 6.5, 0.2 M calcium acetate, 1 % v/v glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 19, 2017 / Details: Adjustable focus K-B pair Si plus Pt, Rh coatings
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.05→103.26 Å / Num. obs: 29535 / % possible obs: 99.3 % / Redundancy: 4.3 % / Rpim(I) all: 0.043 / Rsym value: 0.054 / Net I/σ(I): 13.8
Reflection shellResolution: 2.05→2.11 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.897 / Mean I/σ(I) obs: 1.5 / Num. unique all: 2202 / Rpim(I) all: 0.719 / % possible all: 97.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→103.26 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.938 / SU B: 5.543 / SU ML: 0.146 / Cross valid method: THROUGHOUT / ESU R: 0.213 / ESU R Free: 0.185 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25027 1483 5 %RANDOM
Rwork0.20281 ---
obs0.20519 28028 99.13 %-
Solvent computationIon probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 47.358 Å2
Baniso -1Baniso -2Baniso -3
1-1.84 Å20 Å20 Å2
2--0.16 Å20 Å2
3----2 Å2
Refinement stepCycle: 1 / Resolution: 2.05→103.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3448 0 2 63 3513
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0193498
X-RAY DIFFRACTIONr_bond_other_d0.0020.023108
X-RAY DIFFRACTIONr_angle_refined_deg1.0981.9424747
X-RAY DIFFRACTIONr_angle_other_deg0.87137279
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7535452
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.44827.115156
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.23115590
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.544154
X-RAY DIFFRACTIONr_chiral_restr0.0640.2555
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023934
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02602
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.4214.7021826
X-RAY DIFFRACTIONr_mcbond_other3.4094.7011825
X-RAY DIFFRACTIONr_mcangle_it4.7767.0132272
X-RAY DIFFRACTIONr_mcangle_other4.7757.0152273
X-RAY DIFFRACTIONr_scbond_it3.9945.111672
X-RAY DIFFRACTIONr_scbond_other3.9935.1111673
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.0647.52475
X-RAY DIFFRACTIONr_long_range_B_refined7.93456.1053746
X-RAY DIFFRACTIONr_long_range_B_other7.93356.1143747
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.05→2.104 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 107 -
Rwork0.311 1994 -
obs--97.27 %

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