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- PDB-6aw2: Crystal structure of the HopQ-CEACAM1 complex -

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Basic information

Entry
Database: PDB / ID: 6aw2
TitleCrystal structure of the HopQ-CEACAM1 complex
Components
  • Carcinoembryonic antigen-related cell adhesion molecule 1
  • HopQ
KeywordsCELL ADHESION
Function / homology
Function and homology information


regulation of endothelial cell differentiation / insulin receptor internalization / negative regulation of cytotoxic T cell degranulation / Regulation of MITF-M dependent genes involved in invasion / granulocyte colony-stimulating factor signaling pathway / regulation of homophilic cell adhesion / negative regulation of hepatocyte proliferation / regulation of sprouting angiogenesis / regulation of epidermal growth factor receptor signaling pathway / filamin binding ...regulation of endothelial cell differentiation / insulin receptor internalization / negative regulation of cytotoxic T cell degranulation / Regulation of MITF-M dependent genes involved in invasion / granulocyte colony-stimulating factor signaling pathway / regulation of homophilic cell adhesion / negative regulation of hepatocyte proliferation / regulation of sprouting angiogenesis / regulation of epidermal growth factor receptor signaling pathway / filamin binding / regulation of blood vessel remodeling / negative regulation of natural killer cell mediated cytotoxicity directed against tumor cell target / negative regulation of lipid biosynthetic process / negative regulation of T cell mediated cytotoxicity / regulation of endothelial cell migration / negative regulation of granulocyte differentiation / regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / insulin catabolic process / Fibronectin matrix formation / common myeloid progenitor cell proliferation / cell-cell adhesion via plasma-membrane adhesion molecules / negative regulation of interleukin-1 production / negative regulation of fatty acid biosynthetic process / positive regulation of vasculogenesis / negative regulation of platelet aggregation / bile acid transmembrane transporter activity / negative regulation of vascular permeability / regulation of immune system process / wound healing, spreading of cells / negative regulation of T cell receptor signaling pathway / microvillus membrane / bile acid and bile salt transport / transport vesicle membrane / blood vessel development / homophilic cell adhesion via plasma membrane adhesion molecules / tertiary granule membrane / lateral plasma membrane / regulation of ERK1 and ERK2 cascade / specific granule membrane / regulation of cell migration / protein tyrosine kinase binding / basal plasma membrane / negative regulation of protein kinase activity / integrin-mediated signaling pathway / Cell surface interactions at the vascular wall / adherens junction / regulation of cell growth / kinase binding / cellular response to insulin stimulus / cell junction / cell-cell junction / cell migration / actin binding / protein phosphatase binding / angiogenesis / calmodulin binding / protein dimerization activity / cell adhesion / apical plasma membrane / Neutrophil degranulation / cell surface / signal transduction / protein homodimerization activity / extracellular exosome / identical protein binding / membrane / 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 domain / Immunoglobulin / Immunoglobulin domain / Immunoglobulin domain / Immunoglobulin subtype 2 ...: / SabA, N-terminal extracellular adhesion domain / SabA N-terminal extracellular adhesion domain / Outer membrane protein, Helicobacter / Helicobacter outer membrane protein / Immunoglobulin domain / Immunoglobulin / Immunoglobulin domain / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
HopQ / Cell adhesion molecule CEACAM1
Similarity search - Component
Biological speciesHomo sapiens (human)
Helicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.68 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 1.2Oct 4, 2023Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Carcinoembryonic antigen-related cell adhesion molecule 1
B: HopQ


Theoretical massNumber of molelcules
Total (without water)59,1292
Polymers59,1292
Non-polymers00
Water362
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1970 Å2
ΔGint-14 kcal/mol
Surface area20360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.670, 103.077, 112.881
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number17
Space group name H-MP2221

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Components

#1: Protein Carcinoembryonic antigen-related cell adhesion molecule 1 / Biliary glycoprotein 1 / BGP-1


Mass: 12101.444 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CEACAM1, BGP, BGP1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P13688
#2: 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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 1.95 Å3/Da / Density % sol: 36.97 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 20% PEG 6000, 0.1M HEPES , pH 7.5, 0.2M NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 13, 2017 / Details: Rh coated
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.68→103.08 Å / Num. obs: 13386 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.079 / Net I/σ(I): 10.2
Reflection shellResolution: 2.68→2.81 Å / Redundancy: 4 % / Rmerge(I) obs: 0.818 / Mean I/σ(I) obs: 1.5 / Num. unique all: 1673 / Rpim(I) all: 0.664 / % possible all: 94.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5lp2 2gk2

5lp2

2gk2


Resolution: 2.68→103.08 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.902 / SU B: 19.793 / SU ML: 0.374 / Cross valid method: THROUGHOUT / ESU R Free: 0.395
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS #Refmac command script from PDB_REDO 6.28 # #Use of riding hydrogens make hydrogen ALL #B-factor model selection refi bref ISOT #Solvent ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS #Refmac command script from PDB_REDO 6.28 # #Use of riding hydrogens make hydrogen ALL #B-factor model selection refi bref ISOT #Solvent related settings scal type SIMP lssc function a sigma n solvent YES solvent vdwprobe 1.0 ionprobe 0.9 rshrink 0.9 tlsd waters exclude #Restraint weights weight MATRIX 0.005 temp 1.00
RfactorNum. reflection% reflectionSelection details
Rfree0.27682 660 4.9 %RANDOM
Rwork0.23447 ---
obs0.23657 12702 97.45 %-
Solvent computationIon probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1 Å
Displacement parametersBiso mean: 60.376 Å2
Baniso -1Baniso -2Baniso -3
1--0.25 Å20 Å20 Å2
2--4.61 Å2-0 Å2
3----4.36 Å2
Refinement stepCycle: 1 / Resolution: 2.68→103.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3433 0 0 2 3435
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0193485
X-RAY DIFFRACTIONr_bond_other_d0.0010.023050
X-RAY DIFFRACTIONr_angle_refined_deg1.0281.9414735
X-RAY DIFFRACTIONr_angle_other_deg0.86137142
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7455455
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.327.124153
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.09615574
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.161154
X-RAY DIFFRACTIONr_chiral_restr0.0570.2553
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023942
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_it1.3226.3631835
X-RAY DIFFRACTIONr_mcbond_other1.3186.3621834
X-RAY DIFFRACTIONr_mcangle_it2.2929.5382285
X-RAY DIFFRACTIONr_mcangle_other2.2929.542286
X-RAY DIFFRACTIONr_scbond_it1.2036.3431650
X-RAY DIFFRACTIONr_scbond_other1.2026.3451651
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.0899.492451
X-RAY DIFFRACTIONr_long_range_B_refined3.78675.7643776
X-RAY DIFFRACTIONr_long_range_B_other3.78575.7783777
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.677→2.746 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.37 44 -
Rwork0.344 837 -
obs--90.17 %

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