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- PDB-4znr: Crystal structure of Dln1 complexed with Man(alpha1-3)Man -

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Basic information

Entry
Database: PDB / ID: 4znr
TitleCrystal structure of Dln1 complexed with Man(alpha1-3)Man
ComponentsNatterin-like protein
KeywordsSUGAR BINDING PROTEIN / Pore-forming protein / Aeolysin-like protein / Vetebrate / High-mannose glycans / Complex
Function / homology
Function and homology information


disaccharide binding / pore complex / D-mannose binding / defense response to bacterium / identical protein binding / plasma membrane
Similarity search - Function
: / Jacalin-type lectin domain profile. / Jacalin-like lectin domain / Jacalin-like lectin domain / Jacalin-like lectin domain superfamily
Similarity search - Domain/homology
3alpha-alpha-mannobiose / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Aerolysin-like protein
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsJia, N. / Jiang, Y.L. / Cheng, W. / Wang, H.W. / Zhou, C.Z. / Chen, Y.
Funding support China, 3items
OrganizationGrant numberCountry
the Ministry of Science and Technology of China2013CB835300 China
the Ministry of Science and Technology of China2015CB910100 China
the Ministry of Science and Technology of China2014CB910100 China
CitationJournal: EMBO Rep / Year: 2016
Title: Structural basis for receptor recognition and pore formation of a zebrafish aerolysin-like protein.
Authors: Ning Jia / Nan Liu / Wang Cheng / Yong-Liang Jiang / Hui Sun / Lan-Lan Chen / Junhui Peng / Yonghui Zhang / Yue-He Ding / Zhi-Hui Zhang / Xuejuan Wang / Gang Cai / Junfeng Wang / Meng-Qiu ...Authors: Ning Jia / Nan Liu / Wang Cheng / Yong-Liang Jiang / Hui Sun / Lan-Lan Chen / Junhui Peng / Yonghui Zhang / Yue-He Ding / Zhi-Hui Zhang / Xuejuan Wang / Gang Cai / Junfeng Wang / Meng-Qiu Dong / Zhiyong Zhang / Hui Wu / Hong-Wei Wang / Yuxing Chen / Cong-Zhao Zhou /
Abstract: Various aerolysin-like pore-forming proteins have been identified from bacteria to vertebrates. However, the mechanism of receptor recognition and/or pore formation of the eukaryotic members remains ...Various aerolysin-like pore-forming proteins have been identified from bacteria to vertebrates. However, the mechanism of receptor recognition and/or pore formation of the eukaryotic members remains unknown. Here, we present the first crystal and electron microscopy structures of a vertebrate aerolysin-like protein from Danio rerio, termed Dln1, before and after pore formation. Each subunit of Dln1 dimer comprises a β-prism lectin module followed by an aerolysin module. Specific binding of the lectin module toward high-mannose glycans triggers drastic conformational changes of the aerolysin module in a pH-dependent manner, ultimately resulting in the formation of a membrane-bound octameric pore. Structural analyses combined with computational simulations and biochemical assays suggest a pore-forming process with an activation mechanism distinct from the previously characterized bacterial members. Moreover, Dln1 and its homologs are ubiquitously distributed in bony fishes and lamprey, suggesting a novel fish-specific defense molecule.
History
DepositionMay 5, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 20, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 30, 2016Group: Database references
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 / pdbx_struct_oper_list / 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 / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_oper_list.symmetry_operation / _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 2.1Mar 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Natterin-like protein
B: Natterin-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,09023
Polymers72,9582
Non-polymers3,13221
Water6,648369
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.166, 95.206, 146.112
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Sugars , 2 types, 4 molecules AB

#1: Protein Natterin-like protein


Mass: 36478.879 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: zgc:113413 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5CZR5
#2: Polysaccharide alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose / 3alpha-alpha-mannobiose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: 3alpha-alpha-mannobiose
DescriptorTypeProgram
DManpa1-3DManpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a1122h-1a_1-5]/1-1/a3-b1WURCSPDB2Glycan 1.1.0
[][a-D-Manp]{[(3+1)][a-D-Manp]{}}LINUCSPDB-CARE

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Non-polymers , 8 types, 388 molecules

#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O4
#6: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#7: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#8: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#9: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 369 / 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: 2.72 Å3/Da / Density % sol: 54.86 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 15%(w/v) PEG 6000, 0.1M HEPES pH 7.5, 1.0M LiCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 12, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 45102 / % possible obs: 95.2 % / Redundancy: 4 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 9.8
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.186 / Mean I/σ(I) obs: 5.9 / % possible all: 97.5

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.1→34.57 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.923 / SU B: 4.78 / SU ML: 0.126 / Cross valid method: THROUGHOUT / ESU R: 0.23 / ESU R Free: 0.187 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24114 2265 5 %RANDOM
Rwork0.20652 ---
obs0.20823 42726 95.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.175 Å2
Baniso -1Baniso -2Baniso -3
1--1.33 Å20 Å2-0 Å2
2---2.52 Å20 Å2
3---3.85 Å2
Refinement stepCycle: 1 / Resolution: 2.1→34.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4864 0 205 369 5438
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.025183
X-RAY DIFFRACTIONr_bond_other_d0.0020.024890
X-RAY DIFFRACTIONr_angle_refined_deg1.0581.976964
X-RAY DIFFRACTIONr_angle_other_deg0.612311358
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1565640
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.86425.127197
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.8415858
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.3021511
X-RAY DIFFRACTIONr_chiral_restr0.0650.2780
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025657
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021110
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_it1.3943.5372551
X-RAY DIFFRACTIONr_mcbond_other1.3943.5362550
X-RAY DIFFRACTIONr_mcangle_it2.3135.2933188
X-RAY DIFFRACTIONr_mcangle_other2.3135.2953189
X-RAY DIFFRACTIONr_scbond_it1.63.8532632
X-RAY DIFFRACTIONr_scbond_other1.63.8532632
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.6925.6453775
X-RAY DIFFRACTIONr_long_range_B_refined4.77627.6645534
X-RAY DIFFRACTIONr_long_range_B_other4.67527.4885437
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.101→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 178 -
Rwork0.236 3172 -
obs--97.19 %

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