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- PDB-8pn1: CryoEM structure of Nal1 protein, allele SPIKE, from Oryza sativa... -

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Basic information

Entry
Database: PDB / ID: 8pn1
TitleCryoEM structure of Nal1 protein, allele SPIKE, from Oryza sativa japonica group
ComponentsProtein NARROW LEAF 1
KeywordsPLANT PROTEIN / Serine protease
Function / homologystem vascular tissue pattern formation / internode patterning / regulation of leaf development / leaf vascular tissue pattern formation / Peptidase S1, PA clan / nucleoplasm / cytoplasm / ADENOSINE-5'-TRIPHOSPHATE / Protein NARROW LEAF 1
Function and homology information
Biological speciesOryza sativa Japonica Group (Japanese rice)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.4 Å
AuthorsHuang, L.Y. / Rety, S. / Xi, X.G.
Funding support China, France, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)32071291, 32201042, 32071225, 31870788 China
Centre National de la Recherche Scientifique (CNRS)IRP "Helicase-mediated Gquadruplex DNA unwinding and genome stability" France
CitationJournal: Nat Plants / Year: 2024
Title: The catalytic triad of rice NARROW LEAF1 involves H234.
Authors: Ling-Yun Huang / Na-Nv Liu / Wei-Fei Chen / Xia Ai / Hai-Hong Li / Ze-Lin Zhang / Xi-Miao Hou / Philippe Fossé / Olivier Mauffret / Dong-Sheng Lei / Stephane Rety / Xu-Guang Xi /
Abstract: NARROW LEAF1 (NAL1) exerts a multifaceted influence on leaf morphology and crop yield. Recent crystal study proposed that histidine 233 (H233) is part of the catalytic triad. Here we report that ...NARROW LEAF1 (NAL1) exerts a multifaceted influence on leaf morphology and crop yield. Recent crystal study proposed that histidine 233 (H233) is part of the catalytic triad. Here we report that unlike suggested previously, H234 instead of H233 is a component of the catalytic triad alongside residues D291 and S385 in NAL1. Remarkably, residue 233 unexpectedly plays a pivotal role in regulating NAL1's proteolytic activity. These findings establish a strong foundation for utilizing NAL1 in breeding programs aimed at improving crop yield.
History
DepositionJun 29, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 17, 2024Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2024Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jun 5, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein NARROW LEAF 1
B: Protein NARROW LEAF 1
C: Protein NARROW LEAF 1
D: Protein NARROW LEAF 1
E: Protein NARROW LEAF 1
F: Protein NARROW LEAF 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)286,81118
Polymers283,6226
Non-polymers3,18912
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "D"
d_2ens_1chain "A"
d_3ens_1chain "C"
d_4ens_1chain "B"
d_5ens_1chain "E"
d_6ens_1chain "F"

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ASNASNGLNGLNDD46 - 45721 - 432
d_12ATPATPATPATPDM1001
d_21ASNASNGLNGLNAA46 - 45721 - 432
d_22ATPATPATPATPAG1001
d_31ASNASNGLNGLNCC46 - 45721 - 432
d_32ATPATPATPATPCK1001
d_41ASNASNGLNGLNBB46 - 45721 - 432
d_42ATPATPATPATPBI1001
d_51ASNASNGLNGLNEE46 - 45721 - 432
d_52ATPATPATPATPEO1001
d_61ASNASNGLNGLNFF46 - 45721 - 432
d_62ATPATPATPATPFQ1001

NCS oper:
IDCodeMatrixVector
1given(-0.500177603262, -0.865922833882, -0.000104678850827), (-0.865922828274, 0.500177612784, -0.000105566589952), (0.00014377053845, 3.78417626222E-5, -0.999999988949)260.307460072, 150.255195028, 220.018147292
2given(-0.500108627636, 0.865962095772, -0.00100461458271), (0.865962628053, 0.50010865797, -0.000238828047191), (0.000295600414463, -0.000989398651148, -0.999999466855)69.8892742249, -40.234058867, 220.141428444
3given(0.9999999334, 0.000364948050333, -3.67344597941E-6), (0.000364947566419, -0.999999924841, -0.000130882799684), (-3.72121112588E-6, 0.000130881450352, -0.999999991428)-0.0474659692352, 220.007415572, 220.007056079
4given(-0.500121687972, -0.865955122708, 0.000150584682846), (0.865955133946, -0.500121667956, 0.000152428126545), (-5.66852542724E-5, 0.000206632191146, 0.999999977045)260.270397745, 69.7581624536, -0.0318999936502
5given(-0.500120454465, 0.865955586452, -0.000673289368056), (-0.865955847149, -0.500120340927, 0.000339674166237), (-4.25829664685E-5, 0.00075291686348, 0.999999715651)69.8594322518, 260.259927269, -0.0950232503414

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Components

#1: Protein
Protein NARROW LEAF 1 / Protein GREEN FOR PHOTOSYNTHESIS / Protein QUANTITATIVE TRAIT LOCUS FOR FLAG LEAF WIDTH 4 / qFLW4 / ...Protein GREEN FOR PHOTOSYNTHESIS / Protein QUANTITATIVE TRAIT LOCUS FOR FLAG LEAF WIDTH 4 / qFLW4 / Protein SPIKELET NUMBER


Mass: 47270.379 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa Japonica Group (Japanese rice)
Gene: NAL1, GFP, LSCHL4, SPIKE, Os04g0615000, LOC_Os04g52479, OsJ_16147
Production host: Escherichia coli K-12 (bacteria) / References: UniProt: B4XT64
#2: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Nal1 / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Oryza sativa Japonica Group (Japanese rice)
Source (recombinant)Organism: Escherichia coli K-12 (bacteria)
Buffer solutionpH: 7.5 / Details: 20mM Tris-HCl 100mM NaCl
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 282 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 50000 nm / Nominal defocus min: 5000 nm / Cs: 2.7 mm / Alignment procedure: BASIC
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 49.02 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 700
Image scansMovie frames/image: 32

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Processing

EM software
IDNameVersionCategory
1RELION4particle selection
2SerialEM3.8.4image acquisition
4RELION4CTF correction
7PHENIX1.21rc1_4903model fitting
12RELION43D reconstruction
13PHENIX1.21rc1_4903model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 216590
SymmetryPoint symmetry: D3 (2x3 fold dihedral)
3D reconstructionResolution: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 72613 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model buildingPDB-ID: 8PME

8pme


Accession code: 8PME / Source name: PDB / Type: experimental model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 87.53 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002419266
ELECTRON MICROSCOPYf_angle_d0.579226196
ELECTRON MICROSCOPYf_chiral_restr0.04542910
ELECTRON MICROSCOPYf_plane_restr0.00423396
ELECTRON MICROSCOPYf_dihedral_angle_d5.12442616
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AELECTRON MICROSCOPYNCS constraints3.25989648924E-13
ens_1d_3CELECTRON MICROSCOPYNCS constraints3.80109727356E-13
ens_1d_4BELECTRON MICROSCOPYNCS constraints2.08925752795E-11
ens_1d_5EELECTRON MICROSCOPYNCS constraints2.47656531559E-13
ens_1d_6FELECTRON MICROSCOPYNCS constraints1.14537985155E-11

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