[English] 日本語
Yorodumi
- PDB-6gcj: Solution structure of the RodA hydrophobin from Aspergillus fumigatus -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6gcj
TitleSolution structure of the RodA hydrophobin from Aspergillus fumigatus
ComponentsHydrophobin
KeywordsSTRUCTURAL PROTEIN / Soluble form of the protein that coats Aspergillus fumigatus conidia
Function / homologyFungal hydrophobin / Hydrophobin, conserved site / Fungal hydrophobins signature. / Hydrophobin / Hydrophobins / structural constituent of cell wall / fungal-type cell wall / extracellular region / Hydrophobin
Function and homology information
Biological speciesNeosartorya fumigata (mold)
MethodSOLUTION NMR / simulated annealing
AuthorsPille, A. / Kwan, A. / Aimanianda, V. / Latge, J.-P. / Sunde, M. / Guijarro, J.I.
Funding support France, 2items
OrganizationGrant numberCountry
French National Research AgencyANR-10-BLAN-1309 France
French National Research AgencyANR-16-CE11-0020-01 France
Citation
Journal: Cell Surf / Year: 2019
Title: Assembly and disassembly of Aspergillus fumigatus conidial rodlets
Authors: Valsecchi, I. / Lai, J. / Emmanuel, S.-V. / Pille, A. / Beaussart, A. / Lo, V. / Chi, L. / Pham, L. / Kwan, A.H. / Matondo, M. / Duchateau, M. / Giai-Giannetto, Q. / Aimanianda, V. / ...Authors: Valsecchi, I. / Lai, J. / Emmanuel, S.-V. / Pille, A. / Beaussart, A. / Lo, V. / Chi, L. / Pham, L. / Kwan, A.H. / Matondo, M. / Duchateau, M. / Giai-Giannetto, Q. / Aimanianda, V. / Dufrene, Y. / Bayry, J. / Guijarro, J.I. / Sunde, M. / Latge, J.P.
#1: Journal: Biomol NMR Assign / Year: 2015
Title: (1)H, (13)C and (15)N resonance assignments of the RodA hydrophobin from the opportunistic pathogen Aspergillus fumigatus.
Authors: Pille, A. / Kwan, A.H. / Cheung, I. / Hampsey, M. / Aimanianda, V. / Delepierre, M. / Latge, J.P. / Sunde, M. / Guijarro, J.I.
History
DepositionApr 18, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 27, 2019Provider: repository / Type: Initial release
Revision 1.1May 8, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name
Revision 2.0Sep 4, 2019Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_poly_seq_scheme / 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
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site.label_seq_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.name / _entity.formula_weight / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_end_seq_num / _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_conn.ptnr2_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_end / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_label_seq_id
Revision 2.1Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Hydrophobin


Theoretical massNumber of molelcules
Total (without water)14,5021
Polymers14,5021
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: The diffusion coefficient (NMR), the rotational correlation time (NMR) and the sedimentation coefficient (ultracentrifugatio) agree with a monomer
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7040 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 500structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein Hydrophobin


Mass: 14502.397 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: NMR EXPERIMENTS AND STRUCTURE CALCULATIONS WERE PERFORMED WITH THE PREDICTED FULL-LENGTH PROTEIN (RESIDUES 19-159) AFTER CLEAVAGE OF THE N-TERMINAL SECRETION SIGNAL PEPTIDE (1-18). BECAUSE ...Details: NMR EXPERIMENTS AND STRUCTURE CALCULATIONS WERE PERFORMED WITH THE PREDICTED FULL-LENGTH PROTEIN (RESIDUES 19-159) AFTER CLEAVAGE OF THE N-TERMINAL SECRETION SIGNAL PEPTIDE (1-18). BECAUSE RESIDUES 19-39 ARE DISORDERED, ONLY THE STRUCTURE FOR RESIDUES 39-159 IS DEPOSITED.
Source: (gene. exp.) Neosartorya fumigata (strain CEA10 / CBS 144.89 / FGSC A1163) (mold)
Strain: CEA10 / CBS 144.89 / FGSC A1163 / Gene: AFUB_057130 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: B0Y4B1
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic13D 1H-15N NOESY
121isotropic13D 1H-13C NOESY aliphatic
131isotropic13D 1H-13C NOESY aromatic
151isotropic12D 1H-15N HSQC
161isotropic12D 1H-13C HSQC
141isotropic13D HNCO
171isotropic13D HNCA
191isotropic13D HN(CA)CB
1161isotropic13D C(CCTOCSY) NNH
1111isotropic13D H(CCO)NH
1101isotropic13D (H)CCH-TOCSY
1121isotropic13D HNHA
1131isotropic13D CBCA(CO)NH
1141isotropic12D (HB)CB(CGCD)HD
1151isotropic12D (HB)CB(CGCDCE)HE

-
Sample preparation

DetailsType: solution
Contents: 0.36 mM [U-99% 13C; U-99% 15N] RodA, 90% H2O/10% D2O
Label: 15N_13C_Sample / Solvent system: 90% H2O/10% D2O
SampleConc.: 0.36 mM / Component: RodA / Isotopic labeling: [U-99% 13C; U-99% 15N]
Sample conditionsIonic strength: 20 mM / Ionic strength err: 0.1 / Label: conditions_1 / pH: 4.3 / PH err: 0.05 / Pressure: 1 atm / Temperature: 298.15 K / Temperature err: 0.1

-
NMR measurement

NMR spectrometerType: Agilent NMR System / Manufacturer: Agilent / Model: NMR System / Field strength: 600 MHz / Details: Equipped with a cryoprobe

-
Processing

NMR software
NameVersionDeveloperClassification
VnmrJ4.3Agilentcollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CcpNmr Analysis2.3CCPNdata analysis
ARIA2.3Linge, O'Donoghue and Nilgesstructure calculation
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
TALOS-NShen and Baxstructure calculation
RefinementMethod: simulated annealing / Software ordinal: 5
Details: The structures are based on a total of 2737 restraints, 1590 are unambiguous and 987 ambiguous NOE-derived distances restraints and from 160 dihedral angle constraints derived from Talos-N and HNHA experiment.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 500 / Conformers submitted total number: 10

+
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