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- PDB-4yiq: Structure of the CEACAM6-CEACAM8 heterodimer -

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Basic information

Entry
Database: PDB / ID: 4yiq
TitleStructure of the CEACAM6-CEACAM8 heterodimer
Components
  • Carcinoembryonic antigen-related cell adhesion molecule 6
  • Carcinoembryonic antigen-related cell adhesion molecule 8
KeywordsCELL ADHESION
Function / homology
Function and homology information


positive regulation of endothelial cell-matrix adhesion via fibronectin / Fibronectin matrix formation / positive regulation of heterotypic cell-cell adhesion / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / azurophil granule membrane / homophilic cell adhesion via plasma membrane adhesion molecules / tertiary granule membrane / negative regulation of anoikis / specific granule membrane / side of membrane ...positive regulation of endothelial cell-matrix adhesion via fibronectin / Fibronectin matrix formation / positive regulation of heterotypic cell-cell adhesion / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / azurophil granule membrane / homophilic cell adhesion via plasma membrane adhesion molecules / tertiary granule membrane / negative regulation of anoikis / specific granule membrane / side of membrane / Cell surface interactions at the vascular wall / positive regulation of cell migration / immune response / protein heterodimerization activity / apical plasma membrane / positive regulation of cell population proliferation / Neutrophil degranulation / apoptotic process / cell surface / signal transduction / extracellular space / extracellular exosome / identical protein binding / membrane / plasma membrane
Similarity search - Function
: / 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 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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Carcinoembryonic antigen-related cell adhesion molecule 8 / Carcinoembryonic antigen-related cell adhesion molecule 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 Å
AuthorsBonsor, D.A. / Sundberg, E.J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: Diverse oligomeric states of CEACAM IgV domains.
Authors: Bonsor, D.A. / Gunther, S. / Beadenkopf, R. / Beckett, D. / Sundberg, E.J.
History
DepositionMar 2, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2015Group: Database references
Revision 1.2Nov 4, 2015Group: Database references
Revision 1.3Nov 18, 2015Group: Database references
Revision 1.4Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list / struct_ncs_dom_lim
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _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 8
C: Carcinoembryonic antigen-related cell adhesion molecule 8
B: Carcinoembryonic antigen-related cell adhesion molecule 6
D: Carcinoembryonic antigen-related cell adhesion molecule 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0996
Polymers47,9724
Non-polymers1282
Water3,693205
1
A: Carcinoembryonic antigen-related cell adhesion molecule 8
B: Carcinoembryonic antigen-related cell adhesion molecule 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1134
Polymers23,9862
Non-polymers1282
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1560 Å2
ΔGint-17 kcal/mol
Surface area10300 Å2
MethodPISA
2
C: Carcinoembryonic antigen-related cell adhesion molecule 8
D: Carcinoembryonic antigen-related cell adhesion molecule 6


Theoretical massNumber of molelcules
Total (without water)23,9862
Polymers23,9862
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1640 Å2
ΔGint-10 kcal/mol
Surface area10530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.465, 97.192, 97.691
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12B
22D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLNGLNHISHISAA2 - 1082 - 108
21GLNGLNHISHISCB2 - 1082 - 108
12LYSLYSVALVALBC2 - 1072 - 107
22LYSLYSVALVALDD2 - 1072 - 107

NCS ensembles :
ID
1
2

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Components

#1: Protein Carcinoembryonic antigen-related cell adhesion molecule 8 / CD67 antigen / Carcinoembryonic antigen CGM6 / Non-specific cross-reacting antigen NCA-95


Mass: 12072.521 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CEACAM8, CGM6 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P31997
#2: Protein Carcinoembryonic antigen-related cell adhesion molecule 6 / Non-specific crossreacting antigen / Normal cross-reacting antigen


Mass: 11913.239 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CEACAM6, NCA / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P40199
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 205 / 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: 3.1 Å3/Da / Density % sol: 60.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: Ratio of protein:reservoir = 1:0.2 Reservoir solution; 20% PEG 8000, 0.2 M sodium chloride, 0.1 M Sodium Phosphate/Citric Acid, pH 4.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 28, 2015
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.85→68.9 Å / Num. obs: 51361 / % possible obs: 99.7 % / Redundancy: 6.7 % / Rsym value: 0.091 / Net I/σ(I): 11.3
Reflection shellResolution: 1.85→1.89 Å / Redundancy: 5.9 % / Rmerge(I) obs: 1.341 / Mean I/σ(I) obs: 1.2 / % possible all: 99.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimlessdata scaling
MOLREPphasing
REFMAC5.8.0073refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4Y88 4Y8A

4y88

4y8a


Resolution: 1.85→68.9 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.952 / SU B: 6.574 / SU ML: 0.095 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.114 / ESU R Free: 0.109 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2131 2549 5 %RANDOM
Rwork0.1857 ---
obs0.1871 48753 99.6 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso max: 97.57 Å2 / Biso mean: 33.952 Å2 / Biso min: 16.74 Å2
Baniso -1Baniso -2Baniso -3
1-0.86 Å20 Å20 Å2
2---1.01 Å2-0 Å2
3---0.15 Å2
Refinement stepCycle: final / Resolution: 1.85→68.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3371 0 7 205 3583
Biso mean--44.72 34.87 -
Num. residues----429
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0193484
X-RAY DIFFRACTIONr_bond_other_d0.0040.023285
X-RAY DIFFRACTIONr_angle_refined_deg1.231.9524758
X-RAY DIFFRACTIONr_angle_other_deg0.9537541
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0935439
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.96925.148169
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.89415565
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6421518
X-RAY DIFFRACTIONr_chiral_restr0.0740.2542
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214045
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02813
X-RAY DIFFRACTIONr_mcbond_it1.5071.5441729
X-RAY DIFFRACTIONr_mcbond_other1.5071.5451728
X-RAY DIFFRACTIONr_mcangle_it2.0832.3032159
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.11 Å / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumber
11A6243
12C6243
21B6222
22D6222
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 204 -
Rwork0.299 3525 -
all-3729 -
obs--98.99 %
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)
12.2061-0.6166-0.27491.822-0.46091.58030.10320.28510.2534-0.17020.02980.0595-0.1533-0.1443-0.1330.04830.02740.01720.34180.04290.0556-5.60730.925-18.72
21.97221.10280.35082.9960.3341.21990.03760.15580.0370.1654-0.07260.15330.1976-0.07620.0350.1208-0.07780.02320.34480.02070.014723.95425.151-29.223
32.9445-0.11731.28541.62530.18242.36050.02130.0673-0.15630.02670.0401-0.0886-0.01790.0996-0.06140.0153-0.0090.01650.2359-0.02040.041112.03613.932-9.191
42.36910.2836-0.29621.65390.07061.8359-0.04710.26790.0942-0.15670.0626-0.05380.09650.051-0.01540.0716-0.0574-0.02260.35580.09140.031442.59441.385-37.669
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 108
2X-RAY DIFFRACTION2C2 - 108
3X-RAY DIFFRACTION3B2 - 108
4X-RAY DIFFRACTION4D1 - 108

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