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- PDB-6gbg: Helicobacter pylori adhesin HopQ type I bound to the N-terminal d... -

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Basic information

Entry
Database: PDB / ID: 6gbg
TitleHelicobacter pylori adhesin HopQ type I bound to the N-terminal domain of human CEACAM1
Components
  • Carcinoembryonic antigen-related cell adhesion molecule 1
  • Outer membrane protein
KeywordsCELL ADHESION / Helicobacter pylori / adhesin / Helicobacter outer membrane protein
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 / insulin catabolic process / regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / 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 / negative regulation of protein kinase activity / specific granule membrane / protein tyrosine kinase binding / regulation of cell migration / 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 / identical protein binding / membrane / plasma membrane
Similarity search - Function
: / SabA, N-terminal extracellular adhesion domain / SabA N-terminal extracellular adhesion domain / Outer membrane protein, Helicobacter / Helicobacter outer membrane protein / Immunoglobulin domain / Immunoglobulin / Immunoglobulin domain / Immunoglobulin domain / Immunoglobulin subtype 2 ...: / SabA, N-terminal extracellular adhesion domain / SabA N-terminal extracellular adhesion domain / Outer membrane protein, Helicobacter / Helicobacter outer membrane protein / Immunoglobulin 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
BROMIDE ION / Outer membrane protein / Cell adhesion molecule CEACAM1
Similarity search - Component
Biological speciesHomo sapiens (human)
Helicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsMoonens, K. / Kruse, T. / Gerhard, M. / Remaut, H.
Funding support Belgium, 2items
OrganizationGrant numberCountry
Fonds Wetenschappelijk Onderzoek (FWO)12H8416N Belgium
Fonds Wetenschappelijk Onderzoek (FWO)G033717N Belgium
CitationJournal: EMBO J. / Year: 2018
Title: Helicobacter pyloriadhesin HopQ disruptstransdimerization in human CEACAMs.
Authors: Moonens, K. / Hamway, Y. / Neddermann, M. / Reschke, M. / Tegtmeyer, N. / Kruse, T. / Kammerer, R. / Mejias-Luque, R. / Singer, B.B. / Backert, S. / Gerhard, M. / Remaut, H.
History
DepositionApr 13, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 27, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 11, 2018Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Jan 17, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
D: Carcinoembryonic antigen-related cell adhesion molecule 1
A: Outer membrane protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,4185
Polymers57,1792
Non-polymers2403
Water21612
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS, gel filtration, isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2470 Å2
ΔGint-13 kcal/mol
Surface area19550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.430, 94.430, 119.700
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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


Mass: 12956.362 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CEACAM1, BGP, BGP1 / Production host: Escherichia coli (E. coli) / References: UniProt: P13688
#2: Protein Outer membrane protein


Mass: 44222.402 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (strain G27) (bacteria)
Strain: G27 / Gene: hopQ, HPG27_1120 / Production host: Escherichia coli (E. coli) / References: UniProt: B5Z8H1
#3: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Br
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.7 Å3/Da / Density % sol: 54.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Condition B3 of the Morpheus HT-96 screen (Molecular Dimensions)(0.09 M Halogens mix (0.3M Sodium fluoride; 0.3M Sodium bromide; 0.3M Sodium iodide), 0.1 M Buffer System 1 (1.0M Imidazole; ...Details: Condition B3 of the Morpheus HT-96 screen (Molecular Dimensions)(0.09 M Halogens mix (0.3M Sodium fluoride; 0.3M Sodium bromide; 0.3M Sodium iodide), 0.1 M Buffer System 1 (1.0M Imidazole; MES monohydrate (acid); pH 6.5), 50 % v/v Precipitant Mix 3 (40% v/v Glycerol; 20% w/v PEG 4000)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 28, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.8→67.52 Å / Num. obs: 15692 / % possible obs: 100 % / Redundancy: 10.5 % / Biso Wilson estimate: 73.3 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.147 / Rpim(I) all: 0.047 / Net I/σ(I): 13.6
Reflection shellResolution: 2.8→2.85 Å / Redundancy: 10.7 % / Mean I/σ(I) obs: 1.6 / Num. unique obs: 760 / CC1/2: 0.628 / Rpim(I) all: 0.538 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LP2

5lp2


Resolution: 2.8→67.52 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.905 / SU B: 31.74 / SU ML: 0.291 / Cross valid method: THROUGHOUT / ESU R: 0.799 / ESU R Free: 0.353 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26328 807 5.2 %RANDOM
Rwork0.20131 ---
obs0.20471 14860 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 71.153 Å2
Baniso -1Baniso -2Baniso -3
1-0.64 Å20.32 Å20 Å2
2--0.64 Å2-0 Å2
3----2.08 Å2
Refinement stepCycle: 1 / Resolution: 2.8→67.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3271 0 3 12 3286
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0193328
X-RAY DIFFRACTIONr_bond_other_d0.0010.023119
X-RAY DIFFRACTIONr_angle_refined_deg1.4571.944518
X-RAY DIFFRACTIONr_angle_other_deg0.78237170
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1025426
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.57326.968155
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.26115557
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.315155
X-RAY DIFFRACTIONr_chiral_restr0.0760.2520
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023905
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02756
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_it1.9433.561719
X-RAY DIFFRACTIONr_mcbond_other1.9423.5591718
X-RAY DIFFRACTIONr_mcangle_it3.1565.332137
X-RAY DIFFRACTIONr_mcangle_other3.1565.332138
X-RAY DIFFRACTIONr_scbond_it2.3153.8311609
X-RAY DIFFRACTIONr_scbond_other2.3143.8321610
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.8065.6382381
X-RAY DIFFRACTIONr_long_range_B_refined5.68328.4833753
X-RAY DIFFRACTIONr_long_range_B_other5.68228.4813753
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.39 45 -
Rwork0.27 1100 -
obs--99.74 %
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)
16.1423-4.60069.57676.0503-4.844917.70360.27940.1294-0.2772-0.5874-0.34080.53030.2406-0.66520.06140.3181-0.0041-0.08640.7619-0.10570.3849-35.8778-27.2097-47.3135
22.54750.55051.66860.59210.23893.12410.0471-0.08540.02240.0863-0.1130.09550.02120.08640.06590.2719-0.03050.01370.3338-0.04020.194-9.5143-31.2683-17.2433
37.45561.1855.00973.9923-0.2887.80150.3558-0.3949-0.48080.7874-0.2841-0.09590.40970.3871-0.07180.4463-0.03480.00950.42040.0510.26992.1393-38.0802-2.511
46.48851.33482.78130.9161.22372.7782-0.1419-0.23790.41280.1693-0.0130.0924-0.2450.01580.15490.3385-0.0654-0.00830.3353-0.00110.233-3.3186-25.8454-9.046
51.6445-0.32183.54250.3182-1.253610.46660.1685-0.12-0.13460.07910.04750.23550.4069-0.6348-0.21610.3114-0.08360.06460.4203-0.07090.4222-23.987-33.9888-18.2702
610.01473.19176.49296.29560.587423.42330.1639-0.9691-0.12820.8883-0.2192-0.6445-0.12121.06210.05530.5003-0.01580.01610.6103-0.13120.2866-10.8328-34.46123.4097
74.65160.20080.54331.4401-0.81462.87680.08490.36960.17760.0627-0.12540.03290.0850.2110.04050.2944-0.0331-0.01970.3631-0.06950.1275-7.6592-29.3989-18.9826
814.0044-1.10973.89481.5862-0.3474.52830.03180.10970.43-0.0246-0.1486-0.0393-0.17310.21810.11680.3173-0.0630.01850.3732-0.01350.2089-7.2669-24.6502-27.7591
93.7493-1.11182.04781.3908-0.42332.5667-0.12390.30790.1295-0.0354-0.02280.172-0.2424-0.19260.14670.29760.0336-0.00310.45-0.02810.1964-21.0064-25.6236-37.9116
107.8657-2.678210.02883.0299-3.181918.07520.3040.5274-0.2039-0.2484-0.24530.19460.63430.2566-0.05870.2710.01890.02110.378-0.08260.2639-15.1211-37.5157-35.8028
117.7541-9.08623.553611.4377-2.04017.3870.63290.16780.0041-0.9641-0.3672-0.0759-0.1493-0.2749-0.26560.49380.0722-0.09880.80010.09220.4737-30.3731-19.951-53.5073
125.52461.28131.70599.07763.15655.18880.1974-0.1847-0.18380.41580.0399-0.68430.03450.5625-0.23740.4634-0.0966-0.11570.58230.0810.216629.4449-22.7685.8775
135.19671.62981.45324.2438-1.59611.76150.16220.5243-0.48560.4079-0.028-0.150.1160.5697-0.13420.53860.1737-0.06090.71390.01240.295225.4642-27.6034-3.2303
146.14550.85482.87723.654-0.72331.88820.03080.14470.1497-0.0552-0.09740.19050.13870.10990.06660.3342-0.0378-0.03590.33060.06040.255914.8066-26.2192-4.226
1512.148-2.20738.72144.45520.6798.115-0.1206-1.7097-0.31760.96040.14640.20150.4286-0.7211-0.02580.5423-0.08810.08870.87020.10210.317612.0582-25.52319.7
167.86450.474.86633.64711.756619.1518-0.14090.26980.616-0.2439-0.10640.3278-0.5767-0.2020.24730.363-0.0448-0.05350.26930.00250.314612.9451-19.8052-4.6287
173.38371.99362.51312.74912.38744.7164-0.113-0.41570.36140.3482-0.06890.1664-0.3370.14650.18190.4676-0.0843-0.03870.3973-0.00270.216720.5819-16.89244.1335
1810.05428.3677.15366.98545.80648.56870.2967-0.1821-0.30120.2832-0.1362-0.18820.38030.0504-0.16050.4045-0.02820.02570.33250.06990.363312.4203-33.5192-5.3495
1910.925112.02079.550819.135811.559611.81060.7296-0.9934-0.03131.5947-0.5343-0.3490.49420.0034-0.19530.515-0.0999-0.07770.53460.04910.227127.2392-21.277411.9689
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A54 - 70
2X-RAY DIFFRACTION2A71 - 120
3X-RAY DIFFRACTION3A121 - 144
4X-RAY DIFFRACTION4A145 - 171
5X-RAY DIFFRACTION5A172 - 198
6X-RAY DIFFRACTION6A199 - 212
7X-RAY DIFFRACTION7A213 - 263
8X-RAY DIFFRACTION8A264 - 293
9X-RAY DIFFRACTION9A294 - 380
10X-RAY DIFFRACTION10A381 - 404
11X-RAY DIFFRACTION11A405 - 420
12X-RAY DIFFRACTION12D0 - 16
13X-RAY DIFFRACTION13D17 - 26
14X-RAY DIFFRACTION14D27 - 34
15X-RAY DIFFRACTION15D35 - 42
16X-RAY DIFFRACTION16D43 - 54
17X-RAY DIFFRACTION17D55 - 88
18X-RAY DIFFRACTION18D89 - 98
19X-RAY DIFFRACTION19D99 - 109

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