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- PDB-8pmi: Structure of Nal1 indica cultivar IR64, construct 36-458 in prese... -

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Basic information

Entry
Database: PDB / ID: 8pmi
TitleStructure of Nal1 indica cultivar IR64, construct 36-458 in presence of peptide from FZP protein
ComponentsProtein NARROW LEAF 1
KeywordsPLANT PROTEIN / Serine protease
Function / homology
Function and homology information


stem vascular tissue pattern formation / internode patterning / regulation of leaf development / leaf vascular tissue pattern formation / nucleoplasm / cytoplasm
Similarity search - Function
ADENOSINE-5'-TRIPHOSPHATE / AMMONIUM ION / Protein NARROW LEAF 1
Similarity search - Component
Biological speciesOryza sativa Indica Group (long-grained rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.83 Å
AuthorsHuang, L.Y. / Rety, S. / Xi, X.G.
Funding support China, 4items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32071291 China
National Natural Science Foundation of China (NSFC)32201042 China
National Natural Science Foundation of China (NSFC)32071225 China
National Natural Science Foundation of China (NSFC)31870788 China
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 28, 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)281,66932
Polymers277,2856
Non-polymers4,38426
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27210 Å2
ΔGint-354 kcal/mol
Surface area92860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)174.276, 189.186, 89.922
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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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: 46214.238 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa Indica Group (long-grained rice)
Gene: NAL1, GFP, LSCHL4, SPIKE, Os04g0615000, LOC_Os04g52479, OsJ_16147
Plasmid: pET15b-SUMO / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: B4XT64
#2: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine 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.: 7 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-NH4 / AMMONIUM ION / Ammonium


Mass: 18.038 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H4N
Has ligand of interestY

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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: 2.67 Å3/Da / Density % sol: 53.98 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.05M MES 12% methanol 4% PEG 2000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 23, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.826→94.593 Å / Num. obs: 50605 / % possible obs: 95.1 % / Redundancy: 13.3 % / Biso Wilson estimate: 73.14 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.245 / Rpim(I) all: 0.069 / Rrim(I) all: 0.254 / Net I/σ(I): 9.2
Reflection shellResolution: 2.826→3.132 Å / Rmerge(I) obs: 2.09 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 2530 / CC1/2: 0.588 / Rpim(I) all: 0.608 / Rrim(I) all: 2.178

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSBUILT 20220820data reduction
Aimless0.7.9data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.83→49.5 Å / SU ML: 0.3766 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.8101
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2675 2425 4.79 %
Rwork0.2064 48150 -
obs0.2093 50575 70.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 83.85 Å2
Refinement stepCycle: LAST / Resolution: 2.83→49.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18905 0 254 0 19159
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00319571
X-RAY DIFFRACTIONf_angle_d0.553126624
X-RAY DIFFRACTIONf_chiral_restr0.04242941
X-RAY DIFFRACTIONf_plane_restr0.00393452
X-RAY DIFFRACTIONf_dihedral_angle_d11.47337056
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.83-2.880.384310.32143X-RAY DIFFRACTION1.07
2.88-2.950.283970.3358216X-RAY DIFFRACTION5.38
2.95-3.020.3414250.3171519X-RAY DIFFRACTION13.01
3.02-3.090.2626430.3334969X-RAY DIFFRACTION24.3
3.09-3.170.3369650.29331465X-RAY DIFFRACTION36.53
3.17-3.270.34721180.28932114X-RAY DIFFRACTION53.42
3.27-3.370.37621650.27962778X-RAY DIFFRACTION70.41
3.37-3.490.34521770.26053432X-RAY DIFFRACTION85.72
3.49-3.630.30511940.24294003X-RAY DIFFRACTION99.5
3.63-3.80.28442010.23173983X-RAY DIFFRACTION100
3.8-40.30342050.22574010X-RAY DIFFRACTION100
4-4.250.2442140.19394015X-RAY DIFFRACTION99.98
4.25-4.580.22911950.17274052X-RAY DIFFRACTION99.95
4.58-5.040.26682210.17264043X-RAY DIFFRACTION100
5.04-5.760.25991870.18614075X-RAY DIFFRACTION99.98
5.77-7.260.26291980.21854142X-RAY DIFFRACTION100
7.26-49.50.21742090.17744291X-RAY DIFFRACTION99.67
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)
13.68723056314-0.3369392597231.041313107394.5142557026-3.767791396916.28364967128-0.4621623811520.6959033532030.625947136073-0.0265272359237-0.350797355295-0.976017166392-0.3336863794890.4875356344130.8770411465940.751296039118-0.2705350481220.2675873368260.754436694772-0.1852156875710.82922526929275.697151129835.6558415213-12.7564623132
24.999552299241.078956125650.05871390217773.75088274107-0.09255886214490.831138276019-0.00660209703259-0.04138131011530.380329979544-0.1708212830280.037812007308-0.445722321398-0.5378394847390.259591197127-0.01750113875150.850336531107-0.4122075423520.1138010769030.5007648458860.003995550320670.43687244799956.478635722242.1755365435-10.5763772417
31.663193635290.8872691633230.1965737976052.25448569377-0.2895697930562.37074410425-0.1053047027320.515467017204-0.432362355913-0.2723030818620.278992325701-0.5020042055660.134441364890.462410690239-0.1134209412520.341951870167-0.09381301991160.1328757327160.420063995164-0.1846072849050.31114431702954.117645482718.5208873312-8.34520967388
43.51211657371-2.84495052567-2.91959020057.457989039137.46869943439.39249330131-0.536815852763-0.941474782866-0.6618019375732.18184798862-0.2294126957420.6492954128262.083073798470.102829120110.6246736476051.06676866244-0.232781243992-0.1021172204351.26387143460.3502378483230.8666168515617.0183149251-3.6040655717232.8363754507
58.943257047394.100995958945.367458631564.82598046460.8365319062674.110929952460.2670866025190.624132234004-1.88867016472-0.4018523701540.354502159571-0.6036651101851.214080483060.885740295265-0.6034455523210.520433460436-0.01127916816540.01321847166680.5247118860780.01920495969140.55597270372715.0380664995-10.37650020958.25025765768
63.03459000562-1.81415433875-0.3604322696843.28198809420.9575838210761.29676450507-0.285443135929-0.1010382832020.1134787331170.01534450456110.287051156387-0.3971879620530.04850529995340.128634353843-0.03199258799760.359699314035-0.119956873363-0.05510212468720.267767963509-0.04686097695120.39491308404222.91407959888.292679647817.45561583292
72.29392065732-0.2592754347190.4481094160773.87177168020.1799266339860.942625677209-0.146314050015-0.7795247576980.3298021871240.3435436740330.006493648534560.362766325370.0778409304722-0.2228326488680.1106363187950.258290284664-0.108069549890.08251855282110.507528614187-0.1204392951980.3183239639728.7604483016120.436684372619.5637691937
85.38519746427-0.714156208824-1.900432130123.688890162241.106958252444.33103705821-0.0788868778126-0.8466948781870.342707565936-0.02031810396490.06487460269990.5538506442110.051185011220.0110820342683-0.02115799113550.251993576015-0.179845654914-0.08799231483580.303687567372-0.06256705984290.4939208380387.4754707871618.690678589616.6995003894
97.6501027249-1.446471498060.1903817048165.477085308-0.6190495733581.84562358007-0.239567502686-1.209114714551.421334114270.7740809324630.03671724304281.26056545392-0.282995460925-0.3634416023680.2291128743320.9422018628670.13191418937-0.1265389456150.512144897544-0.3578105943481.9691099556714.324949623474.088714737423.3939555422
101.25586502458-1.66944901768-0.4969408553693.83545262067-0.7681457347991.50337824838-0.256586457968-0.3498231659950.9014323893060.08470355978390.2136178644370.496795225699-0.145993406865-0.0223748165788-0.04007837573880.4702034346160.054698059647-0.3422686942660.410045183836-0.2507786063721.3944587952410.894752005756.511636957116.9798414064
111.541249565960.227727013245-0.372155229381.58323545927-0.1791796997520.692750337386-0.1516420061750.1226271517250.835603903256-0.5625228113350.03696119036660.467161969846-0.329917624233-0.04673908548970.07392899073520.740183416436-0.039131048479-0.3856940669020.3065685964020.02897585641421.2442620154533.353200306664.41534292824.12667008331
122.538362692371.27123525715-1.29280527582.425123962730.06593516289812.45685324173-0.105221746174-0.236928465409-0.8553825557470.0157389079039-0.101459344926-0.3214891227391.537711477050.06719138632890.2658166035431.000879415090.209738442258-0.2054403561120.6512489833210.03880812361231.0923810183163.9604582565-8.5408480902423.8654036344
134.754505754733.00247455058-0.683246102022.59392257230.5540290537141.46998193416-0.00622149645091-0.514863874492-0.505962312484-0.03525397996260.2185267942350.129381915920.465665749583-0.188239793248-0.2012288379510.8129881104090.0922891577149-0.3425807933780.7104097202030.1915187242450.65312473390657.32022232885.247299595536.8586176399
141.870810763310.795119930554-0.2166242500683.29029739255-0.5718691012912.400035922360.0853807536424-0.048166361946-0.5451239924840.04385659151040.143401199285-0.7217642679610.4168333614620.435485770943-0.2067863648020.40052110350.104911702271-0.189249910780.550498900057-0.1252630066910.63090659902674.348747432617.759654665525.1483260881
157.60010425129-5.73284547561-4.824542854264.799057452153.625664406353.057586879560.8834021291450.45974405699-0.228193710413-1.78243082362-1.775099948070.957884110161-0.841510174999-2.233091563861.011107522580.9716635925990.144604283545-0.01759548025381.45271447739-0.200339461190.6184873016143.4431476833432.465134081747.7461396903
169.70551233861.628139646582.710998993894.75481965608-2.628326741153.0445409225-0.423378019342-0.7992138703521.251090454680.8556515088840.02246895174750.635806419258-0.832003161198-0.02282897919590.3225134549560.7129056836270.08930594700610.1267131161961.84347871166-0.4435798613940.80614863501914.970019834445.744721327963.5314314333
171.58136655614-0.274212624235-1.772246578191.63641660482-0.3585040276942.250513404870.348222808225-0.4133190563180.3145334007530.286078034429-0.3303536820880.122978885003-0.542270085619-0.190769813653-0.2031773302740.876765054239-0.07255705721460.1761418692741.59662474786-0.5065605020320.61002449598326.747507416348.818519795456.939119448
181.43309488543-0.04061893255260.6867612790553.484407802170.4157776988742.653391252070.42866338475-0.889162634270.000631971466189-0.269818250367-0.2940063541270.2061527129060.0858274665370.0341830006879-0.1087340798820.621377623696-0.191089040126-0.03901761369951.339519809690.08809701971480.31420300307532.910085190818.896783692348.3140185894
190.655821479362-0.3950494672940.1289387718210.5809788093810.04406660944710.09815106052470.190598701288-0.941753425042-0.2675953328810.247603255682-0.1934686455890.2888773954560.237658459148-0.4053582769990.1324554332560.677827333367-0.2422322216710.1066531500191.76502191347-0.02329816698130.15105103836827.90534543721.385536329851.7449040992
201.569924764660.9358027004580.127133571134.424534714910.623159491811.962244166470.214949530535-0.878302314682-0.2910569402980.0305520320562-0.072143630768-0.05913130964640.193767575425-0.367088258426-0.02062895349020.674871594511-0.1062720360270.1983850923681.543501687640.02969671676930.3579473431328.990304209321.000679211654.8183218899
213.80567552566-3.216348064752.277832210274.24893457538-0.9442035235043.28414989559-0.1566715255570.4011309498713.09065591164-0.5144889245310.0155205933342-1.33663064653-0.9046010314790.9593974955190.1657302160881.09459918709-0.400048235602-0.2507774210980.927857876930.04226196160681.3936864508561.655704863975.049440022512.5877285419
227.5199257139-3.690834177951.484073014359.2540004177-3.689807917275.806917143670.03507978423280.193706623881.93978799372-0.681721935663-0.422625777178-2.12238599456-0.297517303822.06199815520.3540305387960.779755059452-0.227718676509-0.20114894781.016498131530.1451256352271.3823714036183.381579168267.839233461624.6355171349
231.72750385354-0.805636851993-1.180601430481.01866584060.6128939003562.17680235105-0.3247217131630.05236980021440.3387675484020.0395186267827-0.01954531591130.0256269060318-0.119589508366-0.1345398093690.3249714584820.49495928345-0.16005531452-0.2308514083960.834810660776-0.1974890885580.6555593537467.876177024654.102217927431.4656896516
241.37973136440.361588146850.7242364911470.1964461601290.4544953448661.00875902799-0.476910408274-0.5154194192871.397821785090.244726288489-0.1094185466450.216578967607-0.713738629724-0.3811503437490.1773845392890.7910396847690.0388422727342-0.3938181795940.757143476786-0.7252605869641.2261048375450.231380478466.742601565936.6308546776
250.2315830990.00241422302247-0.2635057293993.41436354150.9244929533962.2305832328-0.205304394154-0.3868213429150.8423430432680.158066303015-0.1036686744260.0968685872914-0.4420755965430.21372631610.06104754424360.551879468604-0.111278076847-0.3152684714730.735156407802-0.4202106223171.0643661917758.239654995462.605935992437.7335687594
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 50 through 103 )AA50 - 10315 - 54
22chain 'A' and (resid 104 through 186 )AA104 - 18655 - 137
33chain 'A' and (resid 187 through 457 )AA187 - 457138 - 422
44chain 'B' and (resid 50 through 75 )BD50 - 751 - 26
55chain 'B' and (resid 76 through 103 )BD76 - 10327 - 54
66chain 'B' and (resid 104 through 193 )BD104 - 19355 - 144
77chain 'B' and (resid 194 through 400 )BD194 - 400145 - 351
88chain 'B' and (resid 401 through 458 )BD401 - 458352 - 409
99chain 'C' and (resid 50 through 103 )CG50 - 1031 - 54
1010chain 'C' and (resid 104 through 179 )CG104 - 17955 - 130
1111chain 'C' and (resid 180 through 457 )CG180 - 457131 - 408
1212chain 'D' and (resid 50 through 108 )DJ50 - 1081 - 59
1313chain 'D' and (resid 109 through 186 )DJ109 - 18660 - 137
1414chain 'D' and (resid 187 through 457 )DJ187 - 457138 - 408
1515chain 'E' and (resid 50 through 76 )EM50 - 761 - 27
1616chain 'E' and (resid 77 through 109 )EM77 - 10928 - 60
1717chain 'E' and (resid 110 through 161 )EM110 - 16161 - 112
1818chain 'E' and (resid 162 through 236 )EM162 - 236113 - 187
1919chain 'E' and (resid 237 through 399 )EM237 - 399188 - 350
2020chain 'E' and (resid 400 through 457 )EM400 - 457351 - 408
2121chain 'F' and (resid 50 through 74 )FQ50 - 741 - 25
2222chain 'F' and (resid 75 through 103 )FQ75 - 10326 - 54
2323chain 'F' and (resid 104 through 203 )FQ104 - 20355 - 154
2424chain 'F' and (resid 204 through 353 )FQ204 - 353155 - 304
2525chain 'F' and (resid 354 through 457 )FQ354 - 457305 - 408

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