[English] 日本語
Yorodumi
- PDB-6gbg: Helicobacter pylori adhesin HopQ type I bound to the N-terminal d... -

+
Open data


ID or keywords:

Loading...

-
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 / Regulation of MITF-M dependent genes involved in invasion / granulocyte colony-stimulating factor signaling pathway / regulation of homophilic cell adhesion / negative regulation of hepatocyte proliferation / regulation of sprouting angiogenesis / regulation of epidermal growth factor receptor signaling pathway / filamin binding ...regulation of endothelial cell differentiation / insulin receptor internalization / negative regulation of cytotoxic T cell degranulation / Regulation of MITF-M dependent genes involved in invasion / granulocyte colony-stimulating factor signaling pathway / regulation of homophilic cell adhesion / negative regulation of hepatocyte proliferation / regulation of sprouting angiogenesis / regulation of epidermal growth factor receptor signaling pathway / filamin binding / regulation of blood vessel remodeling / 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 / cell-cell adhesion via plasma-membrane adhesion molecules / negative regulation of interleukin-1 production / negative regulation of fatty acid biosynthetic process / positive regulation of vasculogenesis / 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 / microvillus membrane / bile acid and bile salt transport / transport vesicle membrane / blood vessel development / homophilic cell adhesion via plasma membrane adhesion molecules / tertiary granule membrane / lateral plasma membrane / regulation of ERK1 and ERK2 cascade / specific granule membrane / regulation of cell migration / protein tyrosine kinase binding / basal plasma membrane / negative regulation of protein kinase activity / 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 junction / cell-cell junction / cell migration / actin binding / protein phosphatase binding / angiogenesis / calmodulin binding / protein dimerization activity / cell adhesion / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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)

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

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

Read more