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- PDB-6aw0: Crystal structure of CEACAM3 L44Q -

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Basic information

Entry
Database: PDB / ID: 6aw0
TitleCrystal structure of CEACAM3 L44Q
ComponentsCarcinoembryonic antigen-related cell adhesion molecule 3
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
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
Carcinoembryonic antigen-related cell adhesion molecule 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.43 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)24,5297
Polymers24,1212
Non-polymers4085
Water1,04558
1
B: Carcinoembryonic antigen-related cell adhesion molecule 3
hetero molecules

A: Carcinoembryonic antigen-related cell adhesion molecule 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5297
Polymers24,1212
Non-polymers4085
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_454y-1/2,-x,z-1/41
Buried area1960 Å2
ΔGint-22 kcal/mol
Surface area11020 Å2
MethodPISA
2
A: Carcinoembryonic antigen-related cell adhesion molecule 3
B: Carcinoembryonic antigen-related cell adhesion molecule 3
hetero molecules

A: Carcinoembryonic antigen-related cell adhesion molecule 3
B: Carcinoembryonic antigen-related cell adhesion molecule 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,05814
Polymers48,2424
Non-polymers81610
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_454-x-1/2,y,-z-1/41
Buried area6380 Å2
ΔGint-55 kcal/mol
Surface area19730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.810, 92.810, 155.940
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-202-

CL

21A-333-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: VAL / End label comp-ID: VAL / Refine code: 0 / Auth seq-ID: 1 - 106 / Label seq-ID: 3 - 108

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Carcinoembryonic antigen-related cell adhesion molecule 3 / Carcinoembryonic antigen CGM1


Mass: 12060.540 Da / Num. of mol.: 2 / 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
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 58 / 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: 3.48 Å3/Da / Density % sol: 64.66 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.8M Ammonium Sulphate, 1% PEG 3350, 0.1M Bis Tris pH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jul 14, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.43→79.75 Å / Num. obs: 13227 / % possible obs: 100 % / Redundancy: 7.7 % / Rmerge(I) obs: 0.243 / Rpim(I) all: 0.137 / Net I/σ(I): 8.2
Reflection shellResolution: 2.43→2.62 Å / Redundancy: 7.5 % / Rmerge(I) obs: 1.595 / Mean I/σ(I) obs: 1.2 / Num. unique all: 1351 / Rpim(I) all: 0.913 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
iMOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2QSQ

2qsq


Resolution: 2.43→79.75 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.921 / SU B: 19.017 / SU ML: 0.201 / Cross valid method: THROUGHOUT / ESU R: 0.312 / ESU R Free: 0.227 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24356 670 5.1 %RANDOM
Rwork0.22134 ---
obs0.2225 12487 99.58 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å
Displacement parametersBiso mean: 39.068 Å2
Baniso -1Baniso -2Baniso -3
1-0.66 Å2-0 Å20 Å2
2--0.66 Å2-0 Å2
3----1.33 Å2
Refinement stepCycle: 1 / Resolution: 2.43→79.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1681 0 24 58 1763
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0191734
X-RAY DIFFRACTIONr_bond_other_d0.0020.021565
X-RAY DIFFRACTIONr_angle_refined_deg1.3331.9542354
X-RAY DIFFRACTIONr_angle_other_deg0.87433637
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4175213
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.51325.580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.20915278
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.853154
X-RAY DIFFRACTIONr_chiral_restr0.0750.2271
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021919
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02333
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_it0.2572.502858
X-RAY DIFFRACTIONr_mcbond_other0.2572.502857
X-RAY DIFFRACTIONr_mcangle_it0.4713.7511069
X-RAY DIFFRACTIONr_mcangle_other0.4713.7511070
X-RAY DIFFRACTIONr_scbond_it0.2122.612876
X-RAY DIFFRACTIONr_scbond_other0.2122.612876
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.3633.8861286
X-RAY DIFFRACTIONr_long_range_B_refined2.66728.4561789
X-RAY DIFFRACTIONr_long_range_B_other2.66628.4921790
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 6578 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.05 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.43→2.493 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.373 37 -
Rwork0.358 903 -
obs--100 %
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)
13.01761.88741.09962.87560.57863.73580.11860.0075-0.11490.19710.0664-0.0625-0.21460.2244-0.1850.0622-0.03910.02790.0766-0.04410.0323-5.681727.019-13.6299
22.8912-0.9113-1.73611.94731.21923.94470.0860.1812-0.1519-0.04240.043-0.10180.2010.2482-0.1290.03270.0167-0.00660.1643-0.10960.0786-6.228914.6129-36.1773
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 107
2X-RAY DIFFRACTION2B1 - 107

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