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- PDB-5ya6: Crystal structure of archaeal flagellin FlaB1 from Methanocaldoco... -

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Basic information

Entry
Database: PDB / ID: 5ya6
TitleCrystal structure of archaeal flagellin FlaB1 from Methanocaldococcus jannaschii
ComponentsFlagellin B1
KeywordsSTRUCTURAL PROTEIN / archaea / flagellum / flagellin
Function / homologyarchaeal-type flagellum / Flagellin, archaea / Archaebacterial flagellin / Flagellin/pilin, N-terminal / archaeal or bacterial-type flagellum-dependent cell motility / structural molecule activity / Flagellin B1
Function and homology information
Biological speciesMethanocaldococcus jannaschii DSM 2661 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.5 Å
AuthorsMeshcheryakov, V.A. / Wolf, M.
CitationJournal: EMBO Rep / Year: 2019
Title: High-resolution archaellum structure reveals a conserved metal-binding site.
Authors: Vladimir A Meshcheryakov / Satoshi Shibata / Makoto Tokoro Schreiber / Alejandro Villar-Briones / Kenneth F Jarrell / Shin-Ichi Aizawa / Matthias Wolf /
Abstract: Many archaea swim by means of archaella. While the archaellum is similar in function to its bacterial counterpart, its structure, composition, and evolution are fundamentally different. Archaella are ...Many archaea swim by means of archaella. While the archaellum is similar in function to its bacterial counterpart, its structure, composition, and evolution are fundamentally different. Archaella are related to archaeal and bacterial type IV pili. Despite recent advances, our understanding of molecular processes governing archaellum assembly and stability is still incomplete. Here, we determine the structures of archaella by X-ray crystallography and cryo-EM The crystal structure of FlaB1 is the first and only crystal structure of any archaellin to date at a resolution of 1.5 Å, which is put into biological context by a cryo-EM reconstruction from archaella at 4 Å resolution created with helical single-particle analysis. Our results indicate that the archaellum is predominantly composed of FlaB1. We identify N-linked glycosylation by cryo-EM and mass spectrometry. The crystal structure reveals a highly conserved metal-binding site, which is validated by mass spectrometry and electron energy-loss spectroscopy. We show that the metal-binding site, which appears to be a widespread property of archaellin, is required for filament integrity.
History
DepositionAug 30, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 6, 2019Provider: repository / Type: Initial release
Revision 1.1May 1, 2019Group: Data collection / Database references
Category: citation / citation_author / pdbx_database_related
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 22, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_volume / _citation_author.identifier_ORCID
Revision 2.0Nov 20, 2019Group: Advisory / Atomic model ...Advisory / Atomic model / Database references / Derived calculations / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / entity ...atom_site / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_database_related / pdbx_poly_seq_scheme / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_residues / struct_conf / struct_conn / struct_ref / struct_ref_seq / struct_ref_seq_dif / struct_sheet_range / struct_site_gen
Item: _atom_site.label_seq_id / _entity.formula_weight ..._atom_site.label_seq_id / _entity.formula_weight / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_scientific_name / _pdbx_database_related.content_type / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _struct_conf.beg_label_seq_id / _struct_conf.end_label_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.seq_align_beg / _struct_ref_seq.seq_align_end / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_label_seq_id / _struct_site_gen.label_seq_id
Revision 2.1Mar 27, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Flagellin B1
B: Flagellin B1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9714
Polymers36,8912
Non-polymers802
Water4,468248
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1330 Å2
ΔGint-10 kcal/mol
Surface area14170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.090, 73.660, 107.290
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Flagellin B1


Mass: 18445.539 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii DSM 2661 (archaea)
Strain: DSM 2661 / Gene: flaB1, MJ0891 / Production host: Escherichia coli (E. coli) / References: UniProt: Q58301
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 248 / 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 Å3/Da / Density % sol: 38.61 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / Details: 32.5% PEG4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 30, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→28 Å / Num. obs: 46269 / % possible obs: 96.8 % / Redundancy: 4.3 % / Net I/σ(I): 12.2
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.325 / Mean I/σ(I) obs: 3.3 / CC1/2: 0.883 / % possible all: 92.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MIR / Resolution: 1.5→28 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.951 / SU B: 1.547 / SU ML: 0.056 / Cross valid method: THROUGHOUT / ESU R: 0.076 / ESU R Free: 0.077 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2 2283 4.9 %RANDOM
Rwork0.17273 ---
obs0.17408 43943 96.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 16.921 Å2
Baniso -1Baniso -2Baniso -3
1--0.16 Å20 Å20 Å2
2--1.12 Å20 Å2
3----0.96 Å2
Refinement stepCycle: 1 / Resolution: 1.5→28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2443 0 2 248 2693
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0192524
X-RAY DIFFRACTIONr_bond_other_d0.0020.022361
X-RAY DIFFRACTIONr_angle_refined_deg1.8151.9353457
X-RAY DIFFRACTIONr_angle_other_deg1.04135436
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5995334
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.78925.81105
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.64215378
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.817152
X-RAY DIFFRACTIONr_chiral_restr0.1230.2413
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022936
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02566
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_it1.5621.51318
X-RAY DIFFRACTIONr_mcbond_other1.551.4971317
X-RAY DIFFRACTIONr_mcangle_it2.3172.2441646
X-RAY DIFFRACTIONr_mcangle_other2.3182.2471647
X-RAY DIFFRACTIONr_scbond_it2.4181.7831206
X-RAY DIFFRACTIONr_scbond_other2.4171.7821206
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.682.5671807
X-RAY DIFFRACTIONr_long_range_B_refined5.08513.492884
X-RAY DIFFRACTIONr_long_range_B_other5.02113.0722784
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.272 148 -
Rwork0.263 2972 -
obs--89.6 %

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