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- PDB-6v3p: The BIgI domain of beta protein from S. agalactiae bound to CEACAM1 -

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Basic information

Entry
Database: PDB / ID: 6v3p
TitleThe BIgI domain of beta protein from S. agalactiae bound to CEACAM1
Components
  • Carcinoembryonic antigen-related cell adhesion molecule 1
  • IgA FC receptor
KeywordsCELL ADHESION / Bacterial / Adhesin
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 / negative regulation of hepatocyte proliferation / Regulation of MITF-M dependent genes involved in invasion / filamin binding / regulation of epidermal growth factor receptor signaling pathway / regulation of blood vessel remodeling ...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 / negative regulation of hepatocyte proliferation / Regulation of MITF-M dependent genes involved in invasion / filamin binding / regulation of epidermal growth factor receptor signaling pathway / regulation of blood vessel remodeling / regulation of sprouting angiogenesis / negative regulation of natural killer cell mediated cytotoxicity directed against tumor cell target / negative regulation of lipid biosynthetic process / negative regulation of T cell mediated cytotoxicity / regulation of endothelial cell migration / negative regulation of granulocyte differentiation / regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / insulin catabolic process / Fibronectin matrix formation / common myeloid progenitor cell proliferation / : / negative regulation of interleukin-1 production / positive regulation of vasculogenesis / negative regulation of fatty acid biosynthetic process / negative regulation of platelet aggregation / bile acid transmembrane transporter activity / negative regulation of vascular permeability / regulation of immune system process / wound healing, spreading of cells / negative regulation of T cell receptor signaling pathway / transport vesicle membrane / bile acid and bile salt transport / blood vessel development / microvillus membrane / homophilic cell-cell adhesion / tertiary granule membrane / lateral plasma membrane / regulation of ERK1 and ERK2 cascade / specific granule membrane / negative regulation of protein kinase activity / regulation of cell migration / protein tyrosine kinase binding / basal plasma membrane / integrin-mediated signaling pathway / Cell surface interactions at the vascular wall / adherens junction / regulation of cell growth / kinase binding / cellular response to insulin stimulus / cell-cell junction / cell junction / cell migration / actin binding / angiogenesis / protein phosphatase binding / calmodulin binding / cell adhesion / protein dimerization activity / apical plasma membrane / Neutrophil degranulation / cell surface / signal transduction / protein homodimerization activity / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane
Similarity search - Function
Surface antigen, GAG-binding domain / Surface antigen, GAG-binding domain superfamily / GAG-binding domain on surface antigen / RICH domain / RICH domain superfamily / RICH domain / : / YSIRK type signal peptide / Immunoglobulin domain / YSIRK Gram-positive signal peptide ...Surface antigen, GAG-binding domain / Surface antigen, GAG-binding domain superfamily / GAG-binding domain on surface antigen / RICH domain / RICH domain superfamily / RICH domain / : / YSIRK type signal peptide / Immunoglobulin domain / YSIRK Gram-positive signal peptide / LPXTG cell wall anchor motif / Immunoglobulin / Immunoglobulin domain / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Cell adhesion molecule CEACAM1 / IgA FC receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
Streptococcus agalactiae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.25 Å
AuthorsBonsor, D.A. / McCarthy, A.J.
CitationJournal: Embo J. / Year: 2021
Title: Bacterial protein domains with a novel Ig-like fold target human CEACAM receptors.
Authors: van Sorge, N.M. / Bonsor, D.A. / Deng, L. / Lindahl, E. / Schmitt, V. / Lyndin, M. / Schmidt, A. / Nilsson, O.R. / Brizuela, J. / Boero, E. / Sundberg, E.J. / van Strijp, J.A.G. / Doran, K.S. ...Authors: van Sorge, N.M. / Bonsor, D.A. / Deng, L. / Lindahl, E. / Schmitt, V. / Lyndin, M. / Schmidt, A. / Nilsson, O.R. / Brizuela, J. / Boero, E. / Sundberg, E.J. / van Strijp, J.A.G. / Doran, K.S. / Singer, B.B. / Lindahl, G. / McCarthy, A.J.
History
DepositionNov 26, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 2, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 16, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 11, 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 1
B: Carcinoembryonic antigen-related cell adhesion molecule 1
C: IgA FC receptor
D: IgA FC receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,24511
Polymers52,5804
Non-polymers6657
Water181
1
A: Carcinoembryonic antigen-related cell adhesion molecule 1
hetero molecules

D: IgA FC receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,8598
Polymers26,2902
Non-polymers5686
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_655-x+1,-y,z1
Buried area2280 Å2
ΔGint-54 kcal/mol
Surface area11020 Å2
MethodPISA
2
B: Carcinoembryonic antigen-related cell adhesion molecule 1
C: IgA FC receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3863
Polymers26,2902
Non-polymers961
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1490 Å2
ΔGint-19 kcal/mol
Surface area10770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.616, 131.616, 257.066
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
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
11GLNGLNVALVALAA1 - 1063 - 108
21GLNGLNVALVALBB1 - 1063 - 108
12LYSLYSGLUGLUCC7 - 1098 - 110
22LYSLYSGLUGLUDD7 - 1098 - 110

NCS ensembles :
ID
1
2

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Components

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


Mass: 12101.444 Da / Num. of mol.: 2
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 IgA FC receptor / Beta antigen / B antigen


Mass: 14188.619 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus agalactiae (bacteria) / Gene: bag / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P27951
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O
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: 5.3 Å3/Da / Density % sol: 76.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 1.7M Ammonium Sulfate, 0.1M Sodium Citrate, pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 10, 2018
Details: Mirror: Flat Si Rh coated M0, Kirkpatrick-Baez flat bent Si M1 & M
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.25→38.92 Å / Num. obs: 18198 / % possible obs: 99.8 % / Redundancy: 10.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.025 / Rrim(I) all: 0.082 / Net I/σ(I): 18.2 / Num. measured all: 194550 / Scaling rejects: 13
Reflection shellResolution: 3.25→3.51 Å / Redundancy: 10.9 % / Rmerge(I) obs: 1.411 / Num. unique obs: 3672 / CC1/2: 0.919 / Rpim(I) all: 0.445 / Rrim(I) all: 1.481 / % possible all: 99.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0266refinement
XDSdata reduction
Aimless0.7.4data scaling
MOLREPphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GK2

2gk2


Resolution: 3.25→38.95 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.95 / SU B: 24.846 / SU ML: 0.354 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.675 / ESU R Free: 0.356 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2441 935 5.1 %RANDOM
Rwork0.218 ---
obs0.2194 17226 99.65 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso max: 305.65 Å2 / Biso mean: 149.92 Å2 / Biso min: 110.14 Å2
Baniso -1Baniso -2Baniso -3
1--8.92 Å20 Å2-0 Å2
2---8.92 Å20 Å2
3---17.85 Å2
Refinement stepCycle: final / Resolution: 3.25→38.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3311 0 37 1 3349
Biso mean--215.92 152.4 -
Num. residues----421
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0133393
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173201
X-RAY DIFFRACTIONr_angle_refined_deg1.4221.6544607
X-RAY DIFFRACTIONr_angle_other_deg1.0951.5857393
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.8485417
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.79425.61164
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.85215598
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.736158
X-RAY DIFFRACTIONr_chiral_restr0.0480.2471
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023839
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02721
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A29370.14
12B29370.14
21C28430.16
22D28430.16
LS refinement shellResolution: 3.25→3.334 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.485 74 -
Rwork0.456 1227 -
all-1301 -
obs--99.24 %

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