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- PDB-6gbh: Helicobacter pylori adhesin HopQ type II bound to the N-terminal ... -

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Open data


ID or keywords:

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Basic information

Entry
Database: PDB / ID: 6gbh
TitleHelicobacter pylori adhesin HopQ type II bound to the N-terminal domain of human CEACAM1
Components
  • Carcinoembryonic antigen-related cell adhesion molecule 1
  • HopQ
KeywordsCELL ADHESION / Helicobacter pylori / adhesin / Helicobacter outer membrane protein
Function / homology
Function and homology information


regulation of endothelial cell differentiation / insulin receptor internalization / regulation of homophilic cell adhesion / negative regulation of cytotoxic T cell degranulation / granulocyte colony-stimulating factor signaling pathway / regulation of sprouting angiogenesis / regulation of epidermal growth factor receptor signaling pathway / 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 / regulation of homophilic cell adhesion / negative regulation of cytotoxic T cell degranulation / granulocyte colony-stimulating factor signaling pathway / regulation of sprouting angiogenesis / regulation of epidermal growth factor receptor signaling pathway / 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 / negative regulation of T cell mediated cytotoxicity / bile acid transmembrane transporter activity / 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 / cell-cell adhesion via plasma-membrane adhesion molecules / positive regulation of vasculogenesis / regulation of immune system process / negative regulation of platelet aggregation / bile acid and bile salt transport / negative regulation of vascular permeability / wound healing, spreading of cells / transport vesicle membrane / microvillus 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-cell junction / cell migration / 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 / membrane / identical protein binding / 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 / Immunoglobulin C-2 Type ...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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Carcinoembryonic antigen-related cell adhesion molecule 1 / HopQ
Similarity search - Component
Biological speciesHomo sapiens (human)
Helicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 Å
AuthorsMoonens, K. / Kruse, T. / Gerhard, M. / Remaut, H.
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Carcinoembryonic antigen-related cell adhesion molecule 1
D: Carcinoembryonic antigen-related cell adhesion molecule 1
C: HopQ
A: HopQ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,16012
Polymers116,3924
Non-polymers7698
Water1086
1
B: Carcinoembryonic antigen-related cell adhesion molecule 1
A: HopQ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,5806
Polymers58,1962
Non-polymers3844
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2500 Å2
ΔGint-55 kcal/mol
Surface area19190 Å2
MethodPISA
2
D: Carcinoembryonic antigen-related cell adhesion molecule 1
C: HopQ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,5806
Polymers58,1962
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2530 Å2
ΔGint-58 kcal/mol
Surface area19350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.820, 169.670, 198.096
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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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.: 2
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 HopQ


Mass: 45239.523 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Gene: hopQ / Production host: Escherichia coli (E. coli) / References: UniProt: Q8GDI6
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 2.88 Å3/Da / Density % sol: 57.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Condition A4 of the JB Screen Classic HTS II screen (Jena Bioscience) (1 M Ammonium sulfate, 100 mM Tris; pH 8.5)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.59→99.05 Å / Num. obs: 42047 / % possible obs: 99.6 % / Redundancy: 9.2 % / Biso Wilson estimate: 67.1 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.123 / Rpim(I) all: 0.043 / Net I/σ(I): 11.7
Reflection shellResolution: 2.59→2.66 Å / Redundancy: 9 % / Mean I/σ(I) obs: 0.9 / Num. unique obs: 5934 / CC1/2: 0.605 / % possible all: 97.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LP2, 2GK2

5lp2

2gk2


Resolution: 2.59→99.05 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.932 / SU B: 39.384 / SU ML: 0.348 / Cross valid method: THROUGHOUT / ESU R: 0.401 / ESU R Free: 0.295 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27404 2071 5 %RANDOM
Rwork0.21824 ---
obs0.22099 39448 98.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 93.221 Å2
Baniso -1Baniso -2Baniso -3
1-6.2 Å2-0 Å2-0 Å2
2--1.38 Å20 Å2
3----7.58 Å2
Refinement stepCycle: 1 / Resolution: 2.59→99.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6433 0 40 6 6479
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.026571
X-RAY DIFFRACTIONr_bond_other_d0.0010.026155
X-RAY DIFFRACTIONr_angle_refined_deg1.7391.9438953
X-RAY DIFFRACTIONr_angle_other_deg0.892314133
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6395844
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.03427.4300
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.258151082
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.245158
X-RAY DIFFRACTIONr_chiral_restr0.0920.21068
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.027701
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021475
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_it2.2883.3473400
X-RAY DIFFRACTIONr_mcbond_other2.2893.3473399
X-RAY DIFFRACTIONr_mcangle_it3.6435.0134230
X-RAY DIFFRACTIONr_mcangle_other3.6435.0134231
X-RAY DIFFRACTIONr_scbond_it2.9753.7473170
X-RAY DIFFRACTIONr_scbond_other2.543.6463139
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.1215.3674674
X-RAY DIFFRACTIONr_long_range_B_refined7.35927.1817649
X-RAY DIFFRACTIONr_long_range_B_other7.35827.1827650
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.591→2.659 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.424 146 -
Rwork0.367 2476 -
obs--84.55 %
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)
10.1888-0.46440.2083.9562-6.523213.1338-0.2423-0.4238-0.01720.45880.5010.0705-0.09650.6568-0.25861.41370.469-0.23671.14120.24620.9823-12.8582-19.1388-11.159
21.3737-0.0910.29521.6281-2.0927.0424-0.241-0.0821-0.0010.2941-0.0161-0.42640.2160.68020.25710.98340.224-0.0360.1274-0.05980.7959-12.3769-12.3013-37.5584
35.59610.23353.0252.5517-0.93284.2406-0.19280.44210.3625-0.31670.13930.01940.10470.2130.05351.0153-0.04010.01240.08840.0050.6857-25.8327-1.2096-66.5683
41.82920.26341.12032.03010.32653.7364-0.26740.16380.1726-0.06640.1796-0.2616-0.02560.30760.08780.95350.05080.00260.0448-0.02260.8153-19.5958-2.3607-51.248
51.19240.33040.85483.5568-2.02184.7444-0.22670.06760.29910.2740.0508-0.2766-0.50390.35790.17590.95850.0817-0.03870.0584-0.03010.8417-17.64573.9154-48.0676
61.408-0.38421.02871.8118-0.78174.8709-0.1476-0.0516-0.20210.00860.27740.00460.42290.0346-0.12971.03520.0932-0.00110.0543-0.03030.818-23.5972-14.1937-45.8704
71.0746-0.6390.95582.1124-1.34844.3061-0.0545-0.1462-0.18610.06510.1131-0.1670.57940.2407-0.05861.14720.217-0.02240.0872-0.03550.9083-15.947-19.5338-35.9542
816.4907-3.96764.42223.9288-0.51065.26440.21551.91650.2454-0.67620.0164-0.11180.15310.1805-0.23191.1638-0.4305-0.0290.53660.10950.3262-46.5689-6.7161-92.7663
959.9812-29.515322.073728.3969-11.62788.167-0.0138-0.0361-1.26240.10310.49220.85240.0262-0.0454-0.47831.2294-0.42420.02860.34920.03170.3175-46.951-9.8668-88.336
106.4544-0.84822.74451.3609-0.7394.7483-0.35020.04390.2917-0.44580.5752-0.20950.09470.0545-0.2250.9373-0.2456-0.02150.2825-0.07740.4711-37.3395-5.7786-78.9214
118.4084-9.2311-1.362110.53561.8870.6041-0.6974-1.13830.41280.42470.7894-0.4755-0.1905-0.2794-0.0921.07820.1208-0.17440.86430.02910.5212-46.5858-2.6974-73.2435
1211.8359-6.84494.31865.1409-2.60353.9896-0.324-0.5579-0.2269-0.09590.65020.05120.2619-0.3687-0.32610.977-0.3289-0.06510.36070.04850.3864-47.7553-9.6622-81.4368
137.57242.8599-3.84951.1358-1.19813.5473-0.29490.73141.2679-0.28990.35260.5797-0.6438-0.5048-0.05761.2402-0.224-0.17250.74860.11360.8565-54.64821.5446-87.2939
1413.5535-2.94276.12161.3567-1.46015.9502-0.3950.97831.0528-0.39620.1207-0.55510.16470.69420.27430.974-0.31930.02160.2703-0.05970.5462-33.7226-4.4402-83.29
1526.304915.911923.43459.832713.675322.1227-1.41141.07970.8525-1.39880.63280.44090.1180.8190.77871.6292-0.3494-0.03241.0580.69810.8371-53.137-0.2772-94.6466
1612.31414.43838.73113.05943.431910.18980.025-1.15490.370.5337-0.13490.2268-0.2045-0.34880.10991.05660.1585-0.04420.3778-0.1090.612-7.0834-40.4902-8.2967
171.280.15740.51411.01440.27694.1187-0.1780.1033-0.0751-0.0580.1130.20370.1699-0.22020.0650.87860.0689-0.06130.05230.01040.7746-19.4164-51.9609-45.1476
182.49361.43490.85655.08893.598110.01440.0074-0.0835-0.23680.28120.153-0.00640.5677-0.3014-0.16040.96740.1041-0.0160.050.04830.8489-19.2929-62.6457-36.2558
191.4435-0.43231.20652.381-0.4195.2119-0.16870.06280.2372-0.22430.14330.1904-0.4583-0.2130.02550.91390.0966-0.07130.04410.01490.7489-17.2764-41.9104-47.075
205.8366-3.099710.20451.6843-5.134526.5428-0.19390.02930.01410.23750.0392-0.13120.43520.78290.15470.95980.1476-0.15560.3982-0.01180.8464-4.75-44.7687-24.6903
214.5611.19082.20410.47880.40236.52240.1344-0.7742-0.21140.4305-0.1364-0.26560.03810.59270.0021.19230.167-0.17430.48-0.10090.77095.6116-43.0654-8.2129
223.06240.68723.13151.71451.09146.2692-0.0255-0.18580.14660.0757-0.01130.3055-0.5505-0.27680.03681.00590.2161-0.03240.0591-0.05170.8452-18.3873-37.5162-33.0096
234.2514-0.14172.57881.33140.45635.3008-0.3107-0.52940.44270.30290.0450.0477-0.9839-0.17760.26581.25490.1443-0.06810.0909-0.05480.8839-11.183-34.0277-18.9264
2419.432-0.6286-24.7652.2099-2.396336.37670.21291.4663-0.3015-0.0691-0.17070.4493-0.5368-1.6358-0.04220.9608-0.2223-0.41270.56650.05480.7206-23.9695-46.4268-84.5887
253.7733-0.9921-3.63863.30672.966810.7284-0.25950.8161-0.0056-0.58930.35310.4089-0.2527-0.6505-0.09351.0326-0.2087-0.29320.31370.04440.563-17.1397-46.922-87.1524
264.3897-2.2381-4.07046.36153.58679.4899-0.22570.2191-0.1645-0.30520.11040.2257-0.2115-0.39490.11540.7283-0.015-0.20790.05820.0480.5409-19.6961-47.9647-71.8357
274.5691-0.2476-1.55941.16250.669410.3953-0.52520.1873-0.5357-0.43740.35280.10920.50180.39740.17240.8123-0.0021-0.09450.20940.02980.6059-15.6259-53.0525-71.6453
284.8071-3.8061-3.81087.1535-1.12258.2376-0.6061-0.5525-0.09670.1320.39940.13420.60861.32150.20670.7626-0.0125-0.09030.74850.04970.5828-7.2954-52.6918-74.5212
297.51361.3474-3.2934.62213.097811.3733-0.27590.58160.0182-0.0520.2663-0.05960.25640.30510.00970.9098-0.1717-0.24610.13280.04180.5168-10.5992-47.6943-82.809
303.9415-0.8002-6.66733.42733.361114.46-0.50140.3662-0.2702-0.15540.18010.46650.4068-0.57740.32130.7454-0.0387-0.18720.20610.02780.6184-21.8067-51.6806-74.4237
316.1021-1.674-7.17934.03635.013211.3183-1.20140.9846-0.8803-0.43120.40410.35061.1482-0.74060.79721.2326-0.3741-0.25410.6117-0.11110.7991-18.5755-54.5402-88.9232
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A58 - 66
2X-RAY DIFFRACTION2A67 - 100
3X-RAY DIFFRACTION3A101 - 146
4X-RAY DIFFRACTION4A147 - 177
5X-RAY DIFFRACTION5A178 - 230
6X-RAY DIFFRACTION6A231 - 314
7X-RAY DIFFRACTION7A315 - 412
8X-RAY DIFFRACTION8B1 - 15
9X-RAY DIFFRACTION9B16 - 21
10X-RAY DIFFRACTION10B22 - 53
11X-RAY DIFFRACTION11B54 - 63
12X-RAY DIFFRACTION12B64 - 76
13X-RAY DIFFRACTION13B77 - 83
14X-RAY DIFFRACTION14B84 - 103
15X-RAY DIFFRACTION15B104 - 108
16X-RAY DIFFRACTION16C56 - 80
17X-RAY DIFFRACTION17C81 - 178
18X-RAY DIFFRACTION18C179 - 221
19X-RAY DIFFRACTION19C222 - 282
20X-RAY DIFFRACTION20C283 - 295
21X-RAY DIFFRACTION21C296 - 324
22X-RAY DIFFRACTION22C325 - 373
23X-RAY DIFFRACTION23C374 - 412
24X-RAY DIFFRACTION24D1 - 8
25X-RAY DIFFRACTION25D9 - 25
26X-RAY DIFFRACTION26D26 - 36
27X-RAY DIFFRACTION27D37 - 53
28X-RAY DIFFRACTION28D54 - 64
29X-RAY DIFFRACTION29D65 - 80
30X-RAY DIFFRACTION30D81 - 98
31X-RAY DIFFRACTION31D99 - 108

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Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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