[English] 日本語
Yorodumi
- PDB-8pme: Structure of Nal1 indica cultivar IR64, construct 88-458 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8pme
TitleStructure of Nal1 indica cultivar IR64, construct 88-458
ComponentsNarrow leaf 1
KeywordsPLANT PROTEIN / Serine protease
Function / homologyPeptidase S1, PA clan / ADENOSINE-5'-TRIPHOSPHATE / SUCCINIC ACID / Narrow leaf 1
Function and homology information
Biological speciesOryza sativa Indica Group (long-grained rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.15 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
Revision 1.3Oct 1, 2025Group: Advisory / Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_modification_feature ...pdbx_entry_details / pdbx_modification_feature / pdbx_validate_close_contact / struct_conn
Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Narrow leaf 1
B: Narrow leaf 1
C: Narrow leaf 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,26713
Polymers122,2003
Non-polymers2,06710
Water1,78399
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7710 Å2
ΔGint-48 kcal/mol
Surface area44320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.279, 103.735, 143.471
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

#1: Protein Narrow leaf 1


Mass: 40733.469 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa Indica Group (long-grained rice)
Gene: Nal1 / Plasmid: pET15b-SUMO / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: A0A8K1DE77
#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 3 / 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.: 3 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-SIN / SUCCINIC ACID


Mass: 118.088 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H6O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.43 Å3/Da / Density % sol: 49.28 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M Sodium Hepes-MOPS 0.1M Morpheus Carboxylic acids 37.5% MPD_P1K_P3350 12% 1,6-hexanediol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 29, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.148→84.063 Å / Num. obs: 47522 / % possible obs: 92.5 % / Redundancy: 13 % / Biso Wilson estimate: 49.98 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.025 / Rrim(I) all: 0.09 / Net I/σ(I): 22
Reflection shellResolution: 2.148→2.185 Å / Rmerge(I) obs: 1.545 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 2377 / CC1/2: 0.499 / Rpim(I) all: 0.493 / Rrim(I) all: 1.625 / % possible all: 70.6

-
Processing

Software
NameVersionClassification
PHENIX1.18.2_3874+SVNrefinement
PHENIX1.18.2_3874+SVNrefinement
XDSdata reduction
Aimlessdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.15→39.64 Å / SU ML: 0.2787 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.6553
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2346 2321 4.89 %
Rwork0.1938 45176 -
obs0.1957 47497 72.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 61.56 Å2
Refinement stepCycle: LAST / Resolution: 2.15→39.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7936 0 128 99 8163
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00298209
X-RAY DIFFRACTIONf_angle_d0.772611129
X-RAY DIFFRACTIONf_chiral_restr0.05111256
X-RAY DIFFRACTIONf_plane_restr0.00361435
X-RAY DIFFRACTIONf_dihedral_angle_d14.48312989
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.190.410950.2985123X-RAY DIFFRACTION3.43
2.19-2.240.3697140.3121315X-RAY DIFFRACTION8.67
2.24-2.290.2988350.2998666X-RAY DIFFRACTION18.5
2.29-2.350.3664610.29731030X-RAY DIFFRACTION28.89
2.35-2.410.2999910.28421634X-RAY DIFFRACTION45.39
2.41-2.480.2971320.27692520X-RAY DIFFRACTION69.5
2.48-2.560.331710.28063468X-RAY DIFFRACTION95.64
2.56-2.650.30931860.27163605X-RAY DIFFRACTION100
2.65-2.760.31071110.26682859X-RAY DIFFRACTION78.16
2.76-2.890.27161830.2583637X-RAY DIFFRACTION100
2.89-3.040.31241890.24223649X-RAY DIFFRACTION100
3.04-3.230.29031970.22063609X-RAY DIFFRACTION99.97
3.23-3.480.23671880.2023319X-RAY DIFFRACTION91.02
3.48-3.830.23411900.17563549X-RAY DIFFRACTION96.57
3.83-4.380.18021700.15453589X-RAY DIFFRACTION96.91
4.38-5.520.20071970.14863731X-RAY DIFFRACTION100
5.52-39.640.22010.17563873X-RAY DIFFRACTION99.51
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)
12.305988489942.380255350750.3314744355945.045160977310.5302423763541.69385350292-0.04051482783940.0149436607913-0.1381631378150.02652612636840.0928443431748-0.1916638008860.222275022910.0613992581553-0.0637512965240.2007496169720.0571687690061-0.03761606498210.3276624614010.0185270406220.237052136247-25.960024877612.7569237355131.176497941
22.57945134081.60098413508-0.2870414833334.98193046137-0.03021446353241.35102304327-0.01490380243060.01031667857660.255163688712-0.00536767239467-0.005685001236860.393970427606-0.0030501587606-0.1067584666750.04839927945540.186049162950.0247421726426-0.04504258399670.300745730215-0.0104892041990.259429920692-27.546539148218.2265471375135.451397692
33.602153500541.08531941336-1.11052703089.02691742443-0.001427029794615.006902885630.131497772183-0.1705438319670.416672352195-0.1355137210110.00809252174874-0.722269613321-1.071198304770.746336648174-0.1193413517630.561236588161-0.153646955222-0.01983386473420.435180216675-0.09266656106020.366185612508-7.6838016111555.3726754326121.866016563
40.517148249872-0.18316662039-0.8257223539930.510836631785-1.096835807755.123020265460.169591454115-0.203261213030.1636276722860.240120696286-0.125923866412-0.190654290245-0.2391413833330.301432807213-0.1705142919670.430670205926-0.044991658119-0.03277033855460.354882647361-0.01592189364960.464313222611-10.712910756148.3049602328118.349315089
52.351544282650.6657876674110.2814116362113.437042551260.7998940503735.055207559630.1602038182050.0865358549989-0.0168284168923-0.371076149775-0.0959939919712-0.825776887083-0.147981438690.6652332946770.01006022471210.414190418915-0.04286137829780.2185411080840.3935253443340.0763681535460.572843829687-4.2966197583144.375495209286.8109687724
62.105424420220.165761535031-2.173005717122.31245494150.9626437050226.542023489090.200525533031-0.1923929923610.116035464866-0.3322846864450.19701175583-0.43966456302-0.6838593500310.942907980675-0.3232759380710.476509629172-0.1086001941250.2164128803830.5040172471360.01362892659490.580671989083-1.9021381715848.763064091986.7104266229
73.018125432130.1425879201950.5433046137153.49328961682.152356317927.30244631620.173327977297-0.2477497830630.382225570538-0.0646126207577-0.145010438313-0.104855904016-0.890855275969-0.354925966687-0.0245491168180.3952561736010.00934213337160.124937095410.27748582470.03571892825020.400657870676-13.55208194552.8178619563103.643039918
86.877821312290.589505199616-4.025526368961.39840631940.7563892348783.248711441080.0609063989338-0.426724183988-0.8663484151680.144473783802-0.528258522561-0.3187086039220.4099619482050.9253000466010.3913948674260.637683236702-0.0439502617058-0.0597781342050.3589931830650.008942049577660.487140702821-9.7225376841146.1358496797105.642947336
94.939513377620.719388258094-2.081018155143.97357052474-1.27026275967.904790600050.430769829024-0.05537417158630.852058353909-0.5344447678770.09697106395680.00221371114063-0.7184424289550.61586120715-0.4553954924960.567263629259-0.01845762729670.1025941906240.240093634527-0.02537762564980.43484992038-8.0013798772554.792404408294.9969832701
102.873126587521.33171444035-1.080822899445.792323381670.4362503124982.093282253790.03001831211630.177024943917-0.0116736822184-0.6162682783450.00509248583566-0.00878116814737-0.4611772225230.327340728234-0.02296935911290.491717494747-0.00316186507151-0.04219330339130.4469400590140.02936698536560.205154707377-20.622503820224.257861370670.1268226939
111.306610891931.38247973683-0.8332840029473.2075986023-1.457172357143.127196544920.324484791881-0.395975606304-0.3907246137380.513160136376-0.485846173117-0.5148140056260.08511484487820.413130022880.1724734600240.383864739287-0.0668232168583-0.1523077252530.486373089060.03148689554760.463224699542-29.48172568862.0726119591193.9870527368
122.492381203951.06256102563-0.9226995960382.56544146383-0.5797498225343.059614685650.226898796825-0.103479825595-0.09961068164230.11101407621-0.217673304279-0.151083478605-0.1735952390390.187433241434-0.01912283721660.26653923714-0.0307025704069-0.09829971389220.358184997093-0.01952755055530.301456879776-29.25526930829.0258218490984.9750010331
134.476352558192.65727213536-1.586182900845.24381731048-1.533174930833.83930383844-0.1020953665420.173548652831-0.575471882184-0.201961792121-0.0572069945772-0.03033052279970.6878564411-0.388038638350.1250872320720.38239307282-0.0296355120791-0.1210913319050.430390389939-0.04015851413950.39603494067-36.544845366-5.7559154759883.31461643
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 88 through 273 )AA88 - 2731 - 176
22chain 'A' and (resid 274 through 458 )AA274 - 458177 - 357
33chain 'B' and (resid 88 through 141 )BD88 - 1411 - 54
44chain 'B' and (resid 142 through 192 )BD142 - 19255 - 96
55chain 'B' and (resid 193 through 258 )BD193 - 25897 - 156
66chain 'B' and (resid 259 through 310 )BD259 - 310157 - 188
77chain 'B' and (resid 311 through 399 )BD311 - 399189 - 274
88chain 'B' and (resid 400 through 416 )BD400 - 416275 - 291
99chain 'B' and (resid 417 through 458 )BD417 - 458292 - 333
1010chain 'C' and (resid 88 through 161 )CG88 - 1611 - 74
1111chain 'C' and (resid 162 through 257 )CG162 - 25775 - 153
1212chain 'C' and (resid 258 through 426 )CG258 - 426154 - 311
1313chain 'C' and (resid 427 through 458 )CG427 - 458312 - 343

+
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