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Basic information

Entry
Database: PDB / ID: 5f7n
TitleBlood group antigen binding adhesin BabA of Helicobacter pylori strain 17875 in complex with blood group A Lewis b pentasaccharide
Components
  • Adhesin binding fucosylated histo-blood group antigen
  • Nanobody Nb-ER19
KeywordsCELL ADHESION / Adhesin / Lectin / Nanobody / Complex
Function / homology
Function and homology information


SabA, N-terminal extracellular adhesion domain / SabA N-terminal extracellular adhesion domain / Outer membrane protein, Helicobacter / Helicobacter outer membrane protein / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Blood group A Lewis B antigen, beta anomer / Adhesin binding fucosylated histo-blood group antigen
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
Vicugna pacos (alpaca)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 Å
AuthorsMoonens, K. / Gideonsson, P. / Subedi, S. / Romao, E. / Oscarson, S. / Muyldermans, S. / Boren, T. / Remaut, H.
Funding support Belgium, Sweden, 5items
OrganizationGrant numberCountry
Flanders Institute of Biotechnology (VIB)PRJ9 Belgium
Flanders Science Foundation (FWO)Odysseus program Belgium
Hercules FoundationUABR/09/005 Belgium
Vetenskapsradet/VR Sweden
Cancerfonden Sweden
CitationJournal: Cell Host Microbe / Year: 2016
Title: Structural Insights into Polymorphic ABO Glycan Binding by Helicobacter pylori.
Authors: Moonens, K. / Gideonsson, P. / Subedi, S. / Bugaytsova, J. / Romao, E. / Mendez, M. / Norden, J. / Fallah, M. / Rakhimova, L. / Shevtsova, A. / Lahmann, M. / Castaldo, G. / Brannstrom, K. / ...Authors: Moonens, K. / Gideonsson, P. / Subedi, S. / Bugaytsova, J. / Romao, E. / Mendez, M. / Norden, J. / Fallah, M. / Rakhimova, L. / Shevtsova, A. / Lahmann, M. / Castaldo, G. / Brannstrom, K. / Coppens, F. / Lo, A.W. / Ny, T. / Solnick, J.V. / Vandenbussche, G. / Oscarson, S. / Hammarstrom, L. / Arnqvist, A. / Berg, D.E. / Muyldermans, S. / Boren, T. / Remaut, H.
History
DepositionDec 8, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 20, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2016Group: Database references
Revision 1.2Jun 1, 2016Group: Source and taxonomy
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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: Adhesin binding fucosylated histo-blood group antigen
B: Adhesin binding fucosylated histo-blood group antigen
C: Nanobody Nb-ER19
D: Nanobody Nb-ER19
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,0186
Polymers125,2604
Non-polymers1,7582
Water4,089227
1
A: Adhesin binding fucosylated histo-blood group antigen
C: Nanobody Nb-ER19
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,5093
Polymers62,6302
Non-polymers8791
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3690 Å2
ΔGint20 kcal/mol
Surface area23250 Å2
MethodPISA
2
B: Adhesin binding fucosylated histo-blood group antigen
D: Nanobody Nb-ER19
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,5093
Polymers62,6302
Non-polymers8791
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3710 Å2
ΔGint21 kcal/mol
Surface area23610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.850, 131.950, 123.810
Angle α, β, γ (deg.)90.00, 94.81, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22D

NCS domain segments:

Component-ID: 0 / End auth comp-ID: SER / End label comp-ID: SER / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASNASNAA35 - 46233 - 460
21ASNASNBB35 - 46233 - 460
12VALVALCC3 - 1142 - 113
22VALVALDD3 - 1142 - 113

NCS ensembles :
ID
1
2

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Components

#1: Protein Adhesin binding fucosylated histo-blood group antigen


Mass: 49369.195 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Gene: babA2 / Variant: 17875 / Production host: Escherichia coli (E. coli) / Variant (production host): Top10 / References: UniProt: O52269
#2: Antibody Nanobody Nb-ER19


Mass: 13260.856 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca) / Variant: 17875 / Production host: Escherichia coli (E. coli) / Variant (production host): Top10
#3: Polysaccharide alpha-L-fucopyranose-(1-2)-[2-acetamido-2-deoxy-alpha-D-galactopyranose-(1-3)]beta-D- ...alpha-L-fucopyranose-(1-2)-[2-acetamido-2-deoxy-alpha-D-galactopyranose-(1-3)]beta-D-galactopyranose-(1-3)-[alpha-L-fucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose / Blood group A Lewis B antigen / beta anomer


Type: oligosaccharide, Oligosaccharide / Class: Antigen / Mass: 878.823 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with branches / References: Blood group A Lewis B antigen, beta anomer
DescriptorTypeProgram
LFucpa1-2[DGalpNAca1-3]DGalpb1-3[LFucpa1-4]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,5,4/[a2122h-1b_1-5_2*NCC/3=O][a2112h-1b_1-5][a1221m-1a_1-5][a2112h-1a_1-5_2*NCC/3=O]/1-2-3-4-3/a3-b1_a4-e1_b2-c1_b3-d1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(3+1)][b-D-Galp]{[(2+1)][a-L-Fucp]{}[(3+1)][a-D-GalpNAc]{}}[(4+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 227 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.2 Å3/Da / Density % sol: 61.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2M sodium nitrate, 0.1M Bis Tris propane pH 6.5, 20% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96863 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 21, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96863 Å / Relative weight: 1
ReflectionResolution: 2.28→33.2 Å / Num. obs: 72982 / % possible obs: 98.6 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 12
Reflection shellResolution: 2.28→2.34 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.743 / Mean I/σ(I) obs: 2.2 / % possible all: 97.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5F7K

5f7k


Resolution: 2.28→33.2 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.956 / SU B: 10.901 / SU ML: 0.126 / Cross valid method: THROUGHOUT / ESU R: 0.191 / ESU R Free: 0.159 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19712 3651 5 %RANDOM
Rwork0.17079 ---
obs0.17214 69304 98.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 57.67 Å2
Baniso -1Baniso -2Baniso -3
1-1.12 Å20 Å20.41 Å2
2---1.34 Å20 Å2
3---0.15 Å2
Refinement stepCycle: 1 / Resolution: 2.28→33.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7967 0 120 227 8314
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.028246
X-RAY DIFFRACTIONr_bond_other_d0.0050.027659
X-RAY DIFFRACTIONr_angle_refined_deg1.8631.96311222
X-RAY DIFFRACTIONr_angle_other_deg1.108317616
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.951060
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.67326.046349
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.374151323
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.1731526
X-RAY DIFFRACTIONr_chiral_restr0.1010.21315
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0219552
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021850
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_it2.7683.3214258
X-RAY DIFFRACTIONr_mcbond_other2.7673.324257
X-RAY DIFFRACTIONr_mcangle_it3.9994.9735312
X-RAY DIFFRACTIONr_mcangle_other3.9994.9735313
X-RAY DIFFRACTIONr_scbond_it4.1823.7883988
X-RAY DIFFRACTIONr_scbond_other4.1823.7893989
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.2665.4895911
X-RAY DIFFRACTIONr_long_range_B_refined7.89427.1669302
X-RAY DIFFRACTIONr_long_range_B_other7.89127.0489254
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.09 Å / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumber
11A23144
12B23144
21C6397
22D6397
LS refinement shellResolution: 2.28→2.339 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 242 -
Rwork0.272 5061 -
obs--97.68 %
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)
11.06071.191-0.78583.9562-1.78431.5140.0652-0.05660.0986-0.04410.01080.1992-0.0107-0.019-0.0760.05190.0511-0.01220.2285-0.03760.0194-13.388-20.306-43.301
21.15881.49541.09383.82641.78771.91990.04920.0782-0.1647-0.17940.1553-0.29860.22660.1225-0.20450.110.06260.01040.25440.05220.04721.263-39.4-101.522
31.5820.29920.40015.7846-2.36134.1420.0291-0.0755-0.13540.2762-0.0925-0.2139-0.00170.21990.06340.1415-0.0066-0.04750.22030.01380.0287-8.328-42.766-16.339
42.12460.0664-0.45985.63632.98524.2363-0.06380.06070.12090.2333-0.05070.3531-0.083-0.08960.11450.03640.02840.02040.15170.03040.035111.69-15.373-76.737
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A35 - 462
2X-RAY DIFFRACTION2B34 - 462
3X-RAY DIFFRACTION3C3 - 115
4X-RAY DIFFRACTION4D3 - 117

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