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- PDB-4wtz: Human CEACAM6-CEACAM8 N-domain heterodimer complex -

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Basic information

Entry
Database: PDB / ID: 4wtz
TitleHuman CEACAM6-CEACAM8 N-domain heterodimer complex
Components
  • Carcinoembryonic antigen-related cell adhesion molecule 6
  • Carcinoembryonic antigen-related cell adhesion molecule 8
KeywordsCELL ADHESION / dimer / complex / CEACAM
Function / homology
Function and homology information


positive regulation of endothelial cell-matrix adhesion via fibronectin / Fibronectin matrix formation / regulation of immune system process / positive regulation of heterotypic cell-cell adhesion / azurophil granule membrane / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / homophilic cell adhesion via plasma membrane adhesion molecules / tertiary granule membrane / negative regulation of anoikis / side of membrane ...positive regulation of endothelial cell-matrix adhesion via fibronectin / Fibronectin matrix formation / regulation of immune system process / positive regulation of heterotypic cell-cell adhesion / azurophil granule membrane / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / homophilic cell adhesion via plasma membrane adhesion molecules / tertiary granule membrane / negative regulation of anoikis / side of membrane / specific granule membrane / protein tyrosine kinase binding / Cell surface interactions at the vascular wall / positive regulation of cell migration / immune response / apical plasma membrane / protein heterodimerization activity / apoptotic process / positive regulation of cell population proliferation / Neutrophil degranulation / 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-like domain ...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
NICKEL (II) ION / Carcinoembryonic antigen-related cell adhesion molecule 8 / Carcinoembryonic antigen-related cell adhesion molecule 6 / Carcinoembryonic antigen-related cell adhesion molecule 8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.52 Å
AuthorsKirouac, K.N. / Prive, G.G.
CitationJournal: To Be Published
Title: Human CEACAM6-CEACAM8 N-domain heterodimer complex
Authors: Kirouac, K.N. / Prive, G.G.
History
DepositionOct 30, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 4, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Derived calculations / Refinement description
Category: pdbx_audit_support / pdbx_struct_oper_list / software
Item: _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Sep 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 / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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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 6
B: Carcinoembryonic antigen-related cell adhesion molecule 6
C: Carcinoembryonic antigen-related cell adhesion molecule 6
D: Carcinoembryonic antigen-related cell adhesion molecule 6
E: Carcinoembryonic antigen-related cell adhesion molecule 6
F: Carcinoembryonic antigen-related cell adhesion molecule 6
G: Carcinoembryonic antigen-related cell adhesion molecule 8
H: Carcinoembryonic antigen-related cell adhesion molecule 8
I: Carcinoembryonic antigen-related cell adhesion molecule 8
J: Carcinoembryonic antigen-related cell adhesion molecule 8
K: Carcinoembryonic antigen-related cell adhesion molecule 8
L: Carcinoembryonic antigen-related cell adhesion molecule 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,70915
Polymers144,53312
Non-polymers1763
Water3,495194
1
A: Carcinoembryonic antigen-related cell adhesion molecule 6
J: Carcinoembryonic antigen-related cell adhesion molecule 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2064
Polymers24,0892
Non-polymers1172
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1500 Å2
ΔGint-15 kcal/mol
Surface area10460 Å2
MethodPISA
2
B: Carcinoembryonic antigen-related cell adhesion molecule 6
I: Carcinoembryonic antigen-related cell adhesion molecule 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1483
Polymers24,0892
Non-polymers591
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1410 Å2
ΔGint-9 kcal/mol
Surface area10510 Å2
MethodPISA
3
C: Carcinoembryonic antigen-related cell adhesion molecule 6
G: Carcinoembryonic antigen-related cell adhesion molecule 8


Theoretical massNumber of molelcules
Total (without water)24,0892
Polymers24,0892
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1440 Å2
ΔGint-10 kcal/mol
Surface area10380 Å2
MethodPISA
4
D: Carcinoembryonic antigen-related cell adhesion molecule 6
H: Carcinoembryonic antigen-related cell adhesion molecule 8


Theoretical massNumber of molelcules
Total (without water)24,0892
Polymers24,0892
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1420 Å2
ΔGint-10 kcal/mol
Surface area10460 Å2
MethodPISA
5
E: Carcinoembryonic antigen-related cell adhesion molecule 6
L: Carcinoembryonic antigen-related cell adhesion molecule 8


Theoretical massNumber of molelcules
Total (without water)24,0892
Polymers24,0892
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1520 Å2
ΔGint-9 kcal/mol
Surface area10450 Å2
MethodPISA
6
F: Carcinoembryonic antigen-related cell adhesion molecule 6
K: Carcinoembryonic antigen-related cell adhesion molecule 8


Theoretical massNumber of molelcules
Total (without water)24,0892
Polymers24,0892
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1450 Å2
ΔGint-9 kcal/mol
Surface area10660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.146, 113.582, 123.151
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Carcinoembryonic antigen-related cell adhesion molecule 6 / Non-specific crossreacting antigen / Normal cross-reacting antigen


Mass: 11913.239 Da / Num. of mol.: 6 / Fragment: N domain (UNP residues 34-141)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CEACAM6, NCA / Production host: Escherichia coli (E. coli) / References: UniProt: P40199
#2: Protein
Carcinoembryonic antigen-related cell adhesion molecule 8 / cDNA / FLJ93041 / Homo sapiens carcinoembryonic antigen-related cell adhesionmolecule 8 (CEACAM8) / mRNA


Mass: 12175.664 Da / Num. of mol.: 6 / Fragment: N domain (UNP residues 34-141)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CEACAM8, hCG_21882 / Production host: Escherichia coli (E. coli) / References: UniProt: Q0Z7S6, UniProt: P31997*PLUS
#3: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ni
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 194 / 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: 2.65 Å3/Da / Density % sol: 53.53 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: PEG 2000 MME, NiSO4, Tris-HCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.52→83.49 Å / Num. obs: 52367 / % possible obs: 100 % / Redundancy: 6.7 % / Net I/σ(I): 17.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
d*TREKdata reduction
PDB_EXTRACT3.14data extraction
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4WHC

4whc


Resolution: 2.52→83.49 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.928 / SU B: 22.514 / SU ML: 0.235 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.572 / ESU R Free: 0.272 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2341 1998 3.8 %RANDOM
Rwork0.2053 ---
obs0.2064 50295 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso max: 120.54 Å2 / Biso mean: 29.103 Å2 / Biso min: 16.28 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å2-0 Å2-0 Å2
2---0.41 Å20 Å2
3---0.37 Å2
Refinement stepCycle: final / Resolution: 2.52→83.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10178 0 3 194 10375
Biso mean--70.42 50.94 -
Num. residues----1300
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.01910397
X-RAY DIFFRACTIONr_bond_other_d0.0130.029806
X-RAY DIFFRACTIONr_angle_refined_deg2.0461.9514165
X-RAY DIFFRACTIONr_angle_other_deg2.254322479
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.29551289
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.63925.08500
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.542151676
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.6711554
X-RAY DIFFRACTIONr_chiral_restr0.1280.21614
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02111999
X-RAY DIFFRACTIONr_gen_planes_other0.010.022415
X-RAY DIFFRACTIONr_mcbond_it0.8632.8555195
X-RAY DIFFRACTIONr_mcbond_other0.8632.8555194
X-RAY DIFFRACTIONr_mcangle_it1.4414.2786471
LS refinement shellResolution: 2.521→2.587 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 149 -
Rwork0.314 3661 -
all-3810 -
obs--99.82 %
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)
13.25081.69361.07154.36292.31443.7255-0.29840.25420.2168-0.25950.15560.18250.15570.31230.14280.12670.1123-0.01450.32940.06710.0361-4.68328.306-18.338
23.7247-3.1296-1.01238.37062.56322.7292-0.1546-0.3051-0.40630.11780.23440.64920.11940.1595-0.07980.0214-0.0297-0.00640.31260.08520.1167-20.16628.578-43.696
35.45853.60310.40824.12350.95543.17810.23060.5217-0.1691-0.15690.0981-0.2008-0.27210.0838-0.32880.12970.15150.09590.36130.02930.17726.07226.686-58.094
44.4858-3.0449-0.55274.57070.65112.20390.0291-0.33140.19940.10740.1051-0.2003-0.01150.0465-0.13410.035-0.0322-0.05520.3067-0.00220.125120.43429.937-2.817
55.1684-1.3711-0.01096.9474-1.07666.0439-0.2998-0.2547-0.710.83910.08220.49380.3002-0.28240.21760.1580.07240.08010.3025-0.06930.2318-4.82927.83710.967
64.44730.08470.82515.099-2.12215.4176-0.1649-0.0374-0.65220.4260.1543-0.01690.0263-0.2070.01060.1121-0.0350.1110.2747-0.11460.225835.78627.519-50.141
75.1915-0.4479-1.31283.66710.22016.28060.3413-0.31640.69460.71390.1980.3511-0.8350.0206-0.53930.46840.00130.37680.2176-0.00780.42939.94644.332-38.978
83.3552-0.55170.60694.00230.86024.70920.04380.3306-0.3396-0.55360.03460.36870.2384-0.0335-0.07840.1320.0036-0.11990.2247-0.01660.250223.95412.309-21.828
93.532-0.3193-0.4715.89070.58335.89930.03040.0939-0.0692-0.9807-0.16020.7107-0.5625-0.57180.12980.25830.0367-0.16220.2736-0.05170.2739-34.67748.84-52.939
105.0155-0.0727-0.59267.41350.51736.1644-0.4702-0.1221-0.35990.9093-0.18081.08021.3281-0.57880.65110.6632-0.02840.34040.3141-0.12620.4328-19.9588.555-10.179
116.18450.9938-1.17731.9997-2.08774.3612-0.19-0.6105-1.7511-0.1122-0.24-1.21830.70570.85220.430.52620.20690.03690.61040.14581.446853.53811.973-39.722
126.0837-0.31771.43015.2236-0.39643.0027-0.0726-0.3631-0.75810.91890.0884-0.32910.0488-0.0038-0.01580.7010.1297-0.02520.43110.12660.509812.53711.80722.571
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 107
2X-RAY DIFFRACTION2B0 - 107
3X-RAY DIFFRACTION3C0 - 107
4X-RAY DIFFRACTION4D0 - 107
5X-RAY DIFFRACTION5E0 - 107
6X-RAY DIFFRACTION6F0 - 107
7X-RAY DIFFRACTION7G1 - 108
8X-RAY DIFFRACTION8H0 - 108
9X-RAY DIFFRACTION9I0 - 108
10X-RAY DIFFRACTION10J1 - 108
11X-RAY DIFFRACTION11K0 - 108
12X-RAY DIFFRACTION12L0 - 108

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