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- PDB-8pmg: Structure of Nal1 indica cultivar IR64, construct 36-458 -

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Basic information

Entry
Database: PDB / ID: 8pmg
TitleStructure of Nal1 indica cultivar IR64, construct 36-458
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 / PHOSPHATE ION / Protein NARROW LEAF 1
Similarity search - Component
Biological speciesOryza sativa Indica Group (long-grained rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.29 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)281,06725
Polymers277,2856
Non-polymers3,78219
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25470 Å2
ΔGint-198 kcal/mol
Surface area94340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)173.410, 191.031, 90.253
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.: 6 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
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: 2.7 Å3/Da / Density % sol: 54.37 %
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: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98011 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 13, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98011 Å / Relative weight: 1
ReflectionResolution: 3.29→95.516 Å / Num. obs: 33531 / % possible obs: 88.2 % / Redundancy: 5.8 % / Biso Wilson estimate: 78.58 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.186 / Rpim(I) all: 0.084 / Rrim(I) all: 0.205 / Net I/σ(I): 7.2
Reflection shellResolution: 3.292→3.468 Å / Redundancy: 6.5 % / Rmerge(I) obs: 1.362 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 1678 / CC1/2: 0.721 / Rpim(I) all: 0.573 / Rrim(I) all: 1.481 / % possible all: 83.7

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSBUILT 20200417data reduction
Aimless0.7.4data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.29→65.6 Å / SU ML: 0.4499 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.3839
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2706 1649 4.92 %
Rwork0.2111 31835 -
obs0.2141 33484 72.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 87.24 Å2
Refinement stepCycle: LAST / Resolution: 3.29→65.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18330 0 223 0 18553
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002418940
X-RAY DIFFRACTIONf_angle_d0.641725741
X-RAY DIFFRACTIONf_chiral_restr0.04372862
X-RAY DIFFRACTIONf_plane_restr0.00443329
X-RAY DIFFRACTIONf_dihedral_angle_d12.55566807
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.29-3.390.3186340.315674X-RAY DIFFRACTION18.73
3.39-3.50.3445590.2941312X-RAY DIFFRACTION36.07
3.5-3.620.3172870.27811954X-RAY DIFFRACTION53.49
3.62-3.770.362720.27251184X-RAY DIFFRACTION33
3.77-3.840.325670.27161121X-RAY DIFFRACTION75.52
3.94-4.150.33061840.23763477X-RAY DIFFRACTION97.39
4.15-4.410.25911930.19393616X-RAY DIFFRACTION99.74
4.41-4.750.25371740.18063645X-RAY DIFFRACTION99.56
4.75-5.230.29691860.18353647X-RAY DIFFRACTION99.53
5.23-5.980.26641970.21333684X-RAY DIFFRACTION99.56
5.98-7.530.26091900.24573718X-RAY DIFFRACTION99.49
7.53-65.60.22572060.18583803X-RAY DIFFRACTION98.16
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)
11.275479352710.3999041428220.3273237257511.521847474450.2804907447521.142650308950.131721479322-0.2913079540250.5133854970260.0200209187363-0.09852027583180.149020378283-0.0192459109773-0.2255193157050.01403638838560.5204115306080.08944896632590.07622940211810.629119256593-0.09130535518990.48186450426322.77441.22711.734
23.43475679082-0.317239923122-1.451237163053.44253152112-0.2395449269083.30804161003-0.1176903510910.559793386050.452675320803-0.9898121118240.2472085439850.4561305492910.591225153742-0.241492484985-0.1871876889480.804433078725-0.150369818452-0.09504057672230.5377207825150.04077536933410.45470283041331.3479.906-0.835
32.73014115264-2.09298893672-1.31872512982.552904300270.8940932902532.25650705480.0274527636671-0.298055588333-0.2837939055750.11065164237-0.02385254359840.347924554830.127865393912-0.1455184537990.01381562714280.446423496433-0.09158520546920.01170185330870.508359153470.003443440355280.36945915524728.96322.6399.584
43.115734863192.793888814280.9117724800847.503003212970.8376130093771.13611487948-0.4362997077250.4510820611060.0130290347301-1.269142060520.4575332586310.2188650663010.244381870993-0.458110498957-0.08202317189280.627731181580.04849907320330.1353025223440.678862892147-0.03677688828710.43585126944730.3520.58710.176
52.075192900280.310412659873-1.16159036275-0.457484035209-1.011139133941.28343993265-0.2407077654650.0219668328159-0.337720628448-0.2546885435070.0101725068495-0.05057756611750.8387504662530.06443372765470.1781062772621.109183599670.1481433387570.05117975958730.5408325215250.007078738943640.69256496854662.281-3.236-15.744
63.058928204083.16920865378-1.745140329855.1428704552-1.549522811122.17008322060.193172505024-0.31369366279-0.2425922378280.623452102573-0.266848229071-0.3591978679250.1392074016880.593392587365-0.08815931421870.8694636600870.154773300814-0.09775415905820.5795777166190.01821343815440.41863370329369.02215.481-14.151
70.8887359414130.8562169623911.219895890043.31435883311-1.04703712373.35099490671-1.016864436230.620126168279-0.4655722457290.05822352971480.395991932036-0.1401123515770.862085101957-0.6983190424610.5945937549211.170578637290.07291119699660.1477013524170.80449978757-0.07196546775480.51912971679675.84121.434-32.251
81.063125285392.33167167457-0.4716998511096.2819325462-1.563153810240.525860926733-0.392863391643-0.133963100323-0.31245611122-1.964304804560.08369780410720.06463766373290.9780030781920.4679048404570.2622573257681.208098645640.1130180837440.169229847580.6205110352770.002561829704990.56119752820574.00117.542-28.941
93.600212311351.20014536095-2.078300456225.51331619977-2.127164831252.6191526709-0.207051766923-0.300425993382-0.590165609040.0475770470108-0.318548870102-0.3940391524270.644013462390.8598038852270.4276525403760.7569191831110.2048752300020.1085835522640.8435341625450.05871636717620.45964239511775.14713.972-12.29
108.40165679511-2.21023808653-6.211703027694.335291428740.6725458030135.87966725952-0.4113974251260.152473730265-0.4100616112320.2541955790350.2058064810270.6934083521770.52231078473-0.0694772784535-0.1668166374190.8070732803870.04772310365980.007335418352660.7637446316960.04449917660870.57254130533567.17913.98-13.088
110.9377972433031.395040596750.387658571953.489362221690.7496538277543.08035090779-0.02705030586430.879763850169-0.454441036711-0.3257011442450.287821329292-1.2637221276-0.6465222818821.951320592450.4831812152740.6209395215240.359408531999-0.1333347376570.8806245915630.4613019519750.63556602903884.8515.312-20.929
122.54107363798-1.432396528810.2912588532442.001789175720.1055333626631.063396172670.8811933417650.7131006771331.07383621056-0.00258047247105-0.762616123903-0.283892926783-0.3137677957270.679832212343-0.2317099917990.769849944869-0.1867295915670.002847083191340.9457936617660.1018681649590.78986557863574.11468.757-26.975
133.49793813194-1.3014539795-1.676994160231.454721104570.660146656641.42984028736-0.0640418760657-0.102990567364-0.0212426342483-0.1199604043090.04961530175320.226694905675-0.09583425651180.08088406225450.03614755321670.475462466209-0.1666204511870.00178088888450.515020240603-0.1804326459330.4946693061658.92458.552-10.23
145.65374627798-0.586390025523-1.40057856072.117968564910.6897554134842.63801900128-0.2476744111520.5488865222350.8758709327050.0142699211940.204472713105-0.287026143885-0.001927618024840.17681416252-0.00905791902570.418549487823-0.16202830957-0.06193863665940.49622410252-0.1120822306820.68707275384357.69264.503-9.339
154.96219544681-1.69728249109-2.795352357395.925240733810.4157920738992.012820690140.05860059464-0.1652208643970.3325779240840.175481947784-0.02192976730140.370659118604-0.1578324845460.342121897803-0.0005766473298550.445664124717-0.127864124694-0.07857030834840.583707256771-0.1695413792530.72046027567557.7865.901-4.078
161.82405453314-0.8671963169910.6388076004030.82027154650.0152323231773-0.017058024082-0.07895246126460.532722575488-0.0108279169390.521887295089-0.3240228194790.52148024270.270453856858-0.151550196074-0.03096174177151.1770135949-0.331580234492-0.1552123623780.8394584653860.230133946931.0550125124218.543-7.731-19.029
172.37184102408-1.91117591038-0.9502224817914.282391731111.185139842151.46095894281-0.206470342122-0.269573027039-0.123761427835-0.1171434342990.172438329102-0.05618774428590.105916083612-0.0421323685999-0.06646592705010.513199682561-0.1701935455160.0157794768470.448015788507-0.0396600124740.37889036136216.79410.288-32.644
181.7504411877-0.585699433859-0.5878382231243.609203951611.123594398191.50046794249-0.32003627492-0.1272047906790.09218837980150.2123400633360.436394665681-0.2731132499050.292070833773-0.0672598443782-0.1235233832090.490825406104-0.09789754761650.06381466687690.496983434265-0.04129951975130.32793683015711.22318.663-25.069
193.97482422306-0.334854192175-1.896537475553.238842262070.4231978090412.775698578280.0532398132257-0.3359390443430.428830323094-0.1515155109120.212502906910.01641821444780.152226000239-0.186517874027-0.2337351071950.593259644543-0.1665448555350.006872995773790.508656405384-0.06223373161590.4494921819216.37818.192-29.699
202.88477756688-1.22708504453-0.03958489365793.48941528061-0.6994092273192.54770949968-0.223981920480.4905148585570.410110322240.06767998897470.0372985693921-0.7052170032490.06705884234010.238425517780.1742315839350.468099554015-0.05990206582080.09774203476420.389381798331-0.01784359108540.46343075479569.76136.909-56.782
211.745899842050.273765313020.1327574239722.810176393750.3695838361110.9871513185230.261545743605-0.31227586930.2873906560090.428256976939-0.3877275299820.09486770852350.01932158333490.1884840352810.08787978335840.424390810983-0.1693849826960.06110385003250.547058455175-0.062889475640.28318698153852.5631.218-53.82
224.654034931541.111863599432.744132417043.10062707782-1.49701276253.32636139527-0.0538339949363-1.49417386925-0.4897411577071.778554820130.383293863733-0.6235560005531.12991197708-0.789533511098-0.6090939050791.129931962930.30958742018-0.1970274479820.73303648416-0.129719085820.81105558612159.9129.912-44.189
232.552667464150.740934756017-0.5365694525892.15305083365-0.9863147842692.3445110058-0.02482585936990.222433862428-0.0107684551481-0.171202678881-0.208882682039-0.2642873516460.1070930084920.2829384063790.1539092620450.482039709234-0.06645856371480.001690647611610.447373276473-0.0772558758750.42726237118255.35220.324-53.949
247.92615925761-5.05276648116-0.39421136193.9288742439-0.04730083480742.29430542269-0.624829154487-1.056511303050.626397472480.6908181064710.773609928145-1.20413377501-0.0647294016375-0.116044469477-0.08323513183440.440569850887-0.032923462557-0.006151430549360.416049055491-0.02546344378490.5287388284852.53628.809-53.804
252.875150143341.334302727480.393037130431.46324755686-0.3528115860823.50613538361.20355029011.24337773997-2.75275187899-0.076671487711-0.0192483286518-1.703883488242.451093214120.9422426979271.623536744850.4124918689880.06655318821630.8233556497320.32759531538-0.393276516689-0.26923560751957.43111.626-59.578
263.493310362190.841787995422-0.219012696854-0.36705653686-0.2677972080040.8337620544220.427226195506-0.9692449551043.10906112495-0.262366644144-0.253779179753-0.0791540321372-0.3094129507140.118609501628-0.2031327908681.07640520341-0.00423488139576-0.151236432891.34334667985-0.2467680846991.3179202909117.29974.783-15.488
273.875389624870.40843336905-2.695374176740.6968095279370.7732137494781.963778623490.2106996652120.190955876270.8035036521710.08611812302350.08708712587890.0534060257613-0.0733258941151-0.134963948568-0.2353990309170.4590544384630.16844063125-0.07729240125250.3808997701440.08193098015890.64804231939921.16560.959-33.748
285.15147987577-0.765978594697-2.897451645221.38412542980.0853475903571.81870531870.522026833414-0.6222568519131.4291058207-0.221384071772-0.0827281919079-0.153155539528-0.1281809640240.203693698035-0.3651394743740.531777968240.0429479691529-0.02733974340930.4377850418330.02802615198560.94355592819432.79665.221-36.925
296.159377575061.06932835269-2.773508453055.812620594280.2643758061392.610385003120.331024075178-0.1487022893770.824418919303-0.146661300491-0.1800948073620.371084371956-0.411182989245-0.216496520009-0.1779464074620.5811732815040.07902713428070.06889055069810.5178008607370.09668800216710.70628515328629.3564.562-42.697
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 50:193 )A50 - 193
2X-RAY DIFFRACTION2( CHAIN A AND RESID 194:256 )A194 - 256
3X-RAY DIFFRACTION3( CHAIN A AND RESID 257:399 )A257 - 399
4X-RAY DIFFRACTION4( CHAIN A AND RESID 400:457 )A400 - 457
5X-RAY DIFFRACTION5( CHAIN B AND RESID 50:144 )B50 - 144
6X-RAY DIFFRACTION6( CHAIN B AND RESID 145:220 )B145 - 220
7X-RAY DIFFRACTION7( CHAIN B AND RESID 221:244 )B221 - 244
8X-RAY DIFFRACTION8( CHAIN B AND RESID 245:302 )B245 - 302
9X-RAY DIFFRACTION9( CHAIN B AND RESID 303:400 )B303 - 400
10X-RAY DIFFRACTION10( CHAIN B AND RESID 401:438 )B401 - 438
11X-RAY DIFFRACTION11( CHAIN B AND RESID 439:457 )B439 - 457
12X-RAY DIFFRACTION12( CHAIN C AND RESID 50:113 )C50 - 113
13X-RAY DIFFRACTION13( CHAIN C AND RESID 114:256 )C114 - 256
14X-RAY DIFFRACTION14( CHAIN C AND RESID 257:387 )C257 - 387
15X-RAY DIFFRACTION15( CHAIN C AND RESID 388:458 )C388 - 458
16X-RAY DIFFRACTION16( CHAIN D AND RESID 50:85 )D50 - 85
17X-RAY DIFFRACTION17( CHAIN D AND RESID 86:236 )D86 - 236
18X-RAY DIFFRACTION18( CHAIN D AND RESID 237:387 )D237 - 387
19X-RAY DIFFRACTION19( CHAIN D AND RESID 388:458 )D388 - 458
20X-RAY DIFFRACTION20( CHAIN E AND RESID 50:129 )E50 - 129
21X-RAY DIFFRACTION21( CHAIN E AND RESID 130:220 )E130 - 220
22X-RAY DIFFRACTION22( CHAIN E AND RESID 221:244 )E221 - 244
23X-RAY DIFFRACTION23( CHAIN E AND RESID 245:399 )E245 - 399
24X-RAY DIFFRACTION24( CHAIN E AND RESID 400:438 )E400 - 438
25X-RAY DIFFRACTION25( CHAIN E AND RESID 439:457 )E439 - 457
26X-RAY DIFFRACTION26( CHAIN F AND RESID 50:85 )F50 - 85
27X-RAY DIFFRACTION27( CHAIN F AND RESID 86:236 )F86 - 236
28X-RAY DIFFRACTION28( CHAIN F AND RESID 237:376 )F237 - 376
29X-RAY DIFFRACTION29( CHAIN F AND RESID 377:457 )F377 - 457

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