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- PDB-6aw3: Crystal structure of the HopQ-CEACAM3 L44Q complex -

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Basic information

Entry
Database: PDB / ID: 6aw3
TitleCrystal structure of the HopQ-CEACAM3 L44Q complex
Components
  • Carcinoembryonic antigen-related cell adhesion molecule 3
  • HopQ
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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like ...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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
HopQ / Carcinoembryonic antigen-related cell adhesion molecule 3
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.66 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: HopQ
A: Carcinoembryonic antigen-related cell adhesion molecule 3


Theoretical massNumber of molelcules
Total (without water)59,0882
Polymers59,0882
Non-polymers00
Water1448
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1970 Å2
ΔGint-13 kcal/mol
Surface area20200 Å2
MethodPISA
2
B: HopQ
A: Carcinoembryonic antigen-related cell adhesion molecule 3

B: HopQ
A: Carcinoembryonic antigen-related cell adhesion molecule 3


Theoretical massNumber of molelcules
Total (without water)118,1764
Polymers118,1764
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area6320 Å2
ΔGint-36 kcal/mol
Surface area38030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.830, 102.594, 112.650
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 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) / References: UniProt: H6A3H4
#2: Protein Carcinoembryonic antigen-related cell adhesion molecule 3 / Carcinoembryonic antigen CGM1


Mass: 12060.540 Da / Num. of mol.: 1 / Mutation: L44Q
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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O

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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: 1.9 Å3/Da / Density % sol: 35.22 %
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: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 17, 2017
Details: Rh coated flat bent M0, toroidal focusing post-monochromator M1
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.66→102.59 Å / Num. obs: 13470 / % possible obs: 99.3 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.12 / Rpim(I) all: 0.081 / Net I/σ(I): 10.7
Reflection shellResolution: 2.66→2.79 Å / Redundancy: 5.1 % / Rmerge(I) obs: 1.179 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 1699 / Rpim(I) all: 0.841 / % possible all: 96.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.66→102.59 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.88 / SU B: 44.22 / SU ML: 0.393 / Cross valid method: THROUGHOUT / ESU R Free: 0.414 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29682 661 4.9 %RANDOM
Rwork0.24209 ---
obs0.2448 12792 99.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 53.141 Å2
Baniso -1Baniso -2Baniso -3
1-1.86 Å2-0 Å20 Å2
2---2.45 Å20 Å2
3---0.58 Å2
Refinement stepCycle: 1 / Resolution: 2.66→102.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3367 0 0 8 3375
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0193417
X-RAY DIFFRACTIONr_bond_other_d0.0010.022971
X-RAY DIFFRACTIONr_angle_refined_deg1.141.9394651
X-RAY DIFFRACTIONr_angle_other_deg0.936929
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2835453
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.4126.972142
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.45915536
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.929153
X-RAY DIFFRACTIONr_chiral_restr0.0630.2553
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023884
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02599
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_it0.8933.9651830
X-RAY DIFFRACTIONr_mcbond_other0.8933.9631829
X-RAY DIFFRACTIONr_mcangle_it1.645.9352277
X-RAY DIFFRACTIONr_mcangle_other1.645.9372278
X-RAY DIFFRACTIONr_scbond_it0.6063.8841587
X-RAY DIFFRACTIONr_scbond_other0.6063.8841587
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.1415.8362374
X-RAY DIFFRACTIONr_long_range_B_refined3.13246.793715
X-RAY DIFFRACTIONr_long_range_B_other3.13246.7913716
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.662→2.731 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.259 48 -
Rwork0.387 857 -
obs--92.92 %
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)
10.5485-0.61620.32221.0963-0.57050.5121-0.0632-0.03-0.03380.01430.0188-0.072-0.0641-0.04420.04430.21760.00260.02310.26850.00890.03250.3025-27.3227-3.8816
20.7016-0.24850.25213.2648-0.15331.0492-0.110.04760.0139-0.03040.0512-0.0863-0.1732-0.00680.05880.29680.0179-0.03080.2215-0.00640.0073-12.04813.0495-18.3233
300000000000000-00.1987000.198700.1987000
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B52 - 419
2X-RAY DIFFRACTION2A0 - 107

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