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- PDB-8cxj: The IgI3 domain of R28 protein from S. pyogenes bound to CEACAM1 -

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Basic information

Entry
Database: PDB / ID: 8cxj
TitleThe IgI3 domain of R28 protein from S. pyogenes bound to CEACAM1
Components
  • Carcinoembryonic antigen-related cell adhesion molecule 1
  • Surface protein R28
KeywordsCELL ADHESION / BACTERIAL / ADHESION
Function / homology
Function and homology information


regulation of endothelial cell differentiation / insulin receptor internalization / negative regulation of cytotoxic T cell degranulation / granulocyte colony-stimulating factor signaling pathway / regulation of homophilic cell adhesion / regulation of epidermal growth factor receptor signaling pathway / regulation of sprouting angiogenesis / regulation of blood vessel remodeling / negative regulation of hepatocyte proliferation / negative regulation of natural killer cell mediated cytotoxicity directed against tumor cell target ...regulation of endothelial cell differentiation / insulin receptor internalization / negative regulation of cytotoxic T cell degranulation / granulocyte colony-stimulating factor signaling pathway / regulation of homophilic cell adhesion / regulation of epidermal growth factor receptor signaling pathway / regulation of sprouting angiogenesis / regulation of blood vessel remodeling / negative regulation of hepatocyte proliferation / negative regulation of natural killer cell mediated cytotoxicity directed against tumor cell target / negative regulation of lipid biosynthetic process / bile acid transmembrane transporter activity / negative regulation of T cell mediated cytotoxicity / regulation of endothelial cell migration / filamin binding / negative regulation of granulocyte differentiation / Fibronectin matrix formation / insulin catabolic process / common myeloid progenitor cell proliferation / negative regulation of interleukin-1 production / negative regulation of fatty acid biosynthetic process / positive regulation of vasculogenesis / cell-cell adhesion via plasma-membrane adhesion molecules / regulation of immune system process / negative regulation of platelet aggregation / cell wall / bile acid and bile salt transport / negative regulation of vascular permeability / wound healing, spreading of cells / microvillus membrane / transport vesicle membrane / negative regulation of T cell receptor signaling pathway / regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / blood vessel development / homophilic cell adhesion via plasma membrane adhesion molecules / tertiary granule membrane / lateral plasma membrane / specific granule membrane / regulation of cell migration / protein tyrosine kinase binding / basal plasma membrane / regulation of ERK1 and ERK2 cascade / integrin-mediated signaling pathway / regulation of cell growth / Cell surface interactions at the vascular wall / adherens junction / negative regulation of protein kinase activity / kinase binding / cellular response to insulin stimulus / cell migration / cell-cell junction / cell junction / actin binding / protein phosphatase binding / angiogenesis / protein dimerization activity / calmodulin binding / cell adhesion / apical plasma membrane / Neutrophil degranulation / cell surface / signal transduction / protein homodimerization activity / extracellular exosome / extracellular region / membrane / identical protein binding / plasma membrane
Similarity search - Function
Alpha C protein, N-terminal / AlphaC, C-terminal / ACP, C-terminal domain superfamily / ACP, N-terminal domain superfamily / Alpha C protein N terminal / AlphaC N-terminal domain 2 / Rib/alpha/Esp surface antigen / : / M protein-type anchor domain / YSIRK type signal peptide ...Alpha C protein, N-terminal / AlphaC, C-terminal / ACP, C-terminal domain superfamily / ACP, N-terminal domain superfamily / Alpha C protein N terminal / AlphaC N-terminal domain 2 / Rib/alpha/Esp surface antigen / : / M protein-type anchor domain / YSIRK type signal peptide / Immunoglobulin domain / YSIRK Gram-positive signal peptide / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor 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
Similarity search - Domain/homology
Carcinoembryonic antigen-related cell adhesion molecule 1 / Surface protein R28
Similarity search - Component
Biological speciesHomo sapiens (human)
Streptococcus pyogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.05 Å
AuthorsBonsor, D.A. / McCarthy, A.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/V006495/1 United Kingdom
CitationJournal: Nat Commun / Year: 2023
Title: Human CEACAM1 is targeted by a Streptococcus pyogenes adhesin implicated in puerperal sepsis pathogenesis.
Authors: Catton, E.A. / Bonsor, D.A. / Herrera, C. / Stalhammar-Carlemalm, M. / Lyndin, M. / Turner, C.E. / Soden, J. / van Strijp, J.A.G. / Singer, B.B. / van Sorge, N.M. / Lindahl, G. / McCarthy, A.J.
History
DepositionMay 21, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 15, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 25, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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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 1
C: Carcinoembryonic antigen-related cell adhesion molecule 1
E: Carcinoembryonic antigen-related cell adhesion molecule 1
G: Carcinoembryonic antigen-related cell adhesion molecule 1
D: Surface protein R28
B: Surface protein R28
F: Surface protein R28
H: Surface protein R28
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,48430
Polymers103,5728
Non-polymers1,91222
Water1629
1
A: Carcinoembryonic antigen-related cell adhesion molecule 1
B: Surface protein R28
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4979
Polymers25,8932
Non-polymers6047
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Carcinoembryonic antigen-related cell adhesion molecule 1
D: Surface protein R28
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4979
Polymers25,8932
Non-polymers6047
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Carcinoembryonic antigen-related cell adhesion molecule 1
F: Surface protein R28
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3697
Polymers25,8932
Non-polymers4765
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: Carcinoembryonic antigen-related cell adhesion molecule 1
H: Surface protein R28
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1215
Polymers25,8932
Non-polymers2283
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.962, 76.962, 334.849
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43
Space group name HallP4cw
Symmetry operation#1: x,y,z
#2: -y,x,z+3/4
#3: y,-x,z+1/4
#4: -x,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and resid 1 through 107)
d_2ens_1(chain "C" and resid 1 through 107)
d_3ens_1(chain "E" and resid 1 through 107)
d_4ens_1chain "G"
d_1ens_2(chain "B" and ((resid 1 through 2 and (name N...
d_2ens_2(chain "D" and ((resid 1 through 2 and (name N...
d_3ens_2(chain "F" and ((resid 1 through 2 and (name N...
d_4ens_2(chain "H" and (resid 1 through 58 or (resid 59...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1GLNTYRA1 - 107
d_21ens_1GLNTYRC1 - 107
d_31ens_1GLNTYRE1 - 107
d_41ens_1GLNTYRG1 - 107
d_11ens_2THRLYSD1 - 106
d_21ens_2THRLYSB1 - 106
d_31ens_2THRLYSF1 - 106
d_41ens_2THRLYSH1 - 106

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(0.999906677906, -0.00240343150292, -0.0134483826809), (-0.0026810837772, -0.999782840968, -0.0206659792024), (-0.0133957929777, 0.0207001068506, -0.99969598294)6.59175286731, -4.49969977989, 36.7976942268
2given(-0.935847884553, -0.05848797228, -0.347516753663), (0.0962171004513, -0.991070814165, -0.0923087801399), (-0.339014758614, -0.119824031015, 0.933119067983)69.1837879371, 26.4209220119, 12.7505923416
3given(-0.100950068717, 0.991839515429, 0.0778682172641), (0.928348594818, 0.0657657094922, 0.365846631739), (0.35774008739, 0.109221092692, -0.927411873326)45.8288785187, 1.37328143588, 105.614041686
4given(0.999457198128, -0.0327380630153, 0.00367808929222), (-0.0327476050194, -0.999460362717, 0.00256470721765), (0.0035921409116, -0.00268376370514, -0.999989946917)6.0157824563, -4.59290831414, 36.1150244929
5given(-0.939736613151, -0.00127024512582, -0.341896891448), (0.0225395736566, -0.998047887368, -0.0582441596976), (-0.341155485847, -0.0624403795378, 0.937930772221)69.4085729938, 26.7474087275, 13.0356599849
6given(-0.0426887794511, 0.996758294595, 0.0681950897487), (0.939105960046, 0.0167376390373, 0.343219823502), (0.340965781149, 0.0786940505776, -0.936776164561)44.8773085506, 1.62279895847, 106.336268848

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Components

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Protein , 2 types, 8 molecules ACEGDBFH

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


Mass: 12101.444 Da / Num. of mol.: 4
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) / References: UniProt: P13688
#2: Protein
Surface protein R28 /


Mass: 13791.591 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pyogenes (bacteria) / Gene: spr28 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9XDB6

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Non-polymers , 4 types, 31 molecules

#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 4.79 Å3/Da / Density % sol: 74.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 1.45 M Ammonium sulfate 0.1M Na/K Phosphate pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1.1271 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 16, 2019
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1271 Å / Relative weight: 1
ReflectionResolution: 3.05→38.96 Å / Num. obs: 36722 / % possible obs: 99.9 % / Redundancy: 6.2 % / Biso Wilson estimate: 89.1 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.051 / Net I/σ(I): 16
Reflection shellResolution: 3.05→3.19 Å / Num. unique obs: 4528 / CC1/2: 0.828

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Processing

Software
NameVersionClassification
REFMAC7.1.016refinement
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6V3P

6v3p


Resolution: 3.05→38.96 Å / SU ML: 0.4802 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.2538
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2376 1925 5.24 %
Rwork0.2074 34797 -
obs0.209 36722 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 102.07 Å2
Refinement stepCycle: LAST / Resolution: 3.05→38.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6614 0 103 9 6726
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00216799
X-RAY DIFFRACTIONf_angle_d0.5299250
X-RAY DIFFRACTIONf_chiral_restr0.04561091
X-RAY DIFFRACTIONf_plane_restr0.00421188
X-RAY DIFFRACTIONf_dihedral_angle_d15.42372501
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.659893195139
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS0.92513069978
ens_1d_4AX-RAY DIFFRACTIONTorsion NCS0.924123165194
ens_2d_2BX-RAY DIFFRACTIONTorsion NCS0.767545233295
ens_2d_3BX-RAY DIFFRACTIONTorsion NCS0.801236265179
ens_2d_4BX-RAY DIFFRACTIONTorsion NCS0.759240569794
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.05-3.130.42091460.38432481X-RAY DIFFRACTION99.13
3.13-3.210.35041520.35642463X-RAY DIFFRACTION99.47
3.21-3.310.37331470.31772443X-RAY DIFFRACTION99.31
3.31-3.410.31161370.28752480X-RAY DIFFRACTION99.66
3.41-3.530.30641320.27082487X-RAY DIFFRACTION99.66
3.53-3.680.31561590.24582440X-RAY DIFFRACTION99.65
3.68-3.840.27321100.25452544X-RAY DIFFRACTION99.59
3.84-4.040.28051220.22962511X-RAY DIFFRACTION100
4.04-4.30.21981430.19282463X-RAY DIFFRACTION99.85
4.3-4.630.21481270.16692483X-RAY DIFFRACTION99.96
4.63-5.090.19461580.17042486X-RAY DIFFRACTION99.96
5.09-5.830.21711390.1822476X-RAY DIFFRACTION99.89
5.83-7.340.21391150.1992522X-RAY DIFFRACTION99.81
7.34-38.960.1711380.15522518X-RAY DIFFRACTION99.74
Refinement TLS params.Method: refined / Origin x: 33.195 Å / Origin y: 16.371 Å / Origin z: 38.682 Å
111213212223313233
T0.72 Å20.0107 Å2-0.035 Å2-0.618 Å2-0.0249 Å2--0.67 Å2
L0.1069 °2-0.1043 °2-0.392 °2-0.694 °20.878 °2--1.312 °2
S0.0387 Å °-0.0502 Å °-0.0262 Å °-0.148 Å °-0.067 Å °-0.042 Å °0.0243 Å °0.028 Å °0.029 Å °
Refinement TLS groupSelection details: all

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