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- PDB-9x5i: Crystal structure of Medicago truncatula DELLA1-GRAS domain -

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Basic information

Entry
Database: PDB / ID: 9x5i
TitleCrystal structure of Medicago truncatula DELLA1-GRAS domain
ComponentsDELLA protein 1
KeywordsPLANT PROTEIN / Transcription factor
Function / homology
Function and homology information


response to symbiotic fungus / arbuscular mycorrhizal association / regulation of seed dormancy process / negative regulation of seed germination / negative regulation of gibberellic acid mediated signaling pathway / gibberellic acid mediated signaling pathway / response to abscisic acid / cellular response to phosphate starvation / sequence-specific DNA binding / DNA-binding transcription factor activity ...response to symbiotic fungus / arbuscular mycorrhizal association / regulation of seed dormancy process / negative regulation of seed germination / negative regulation of gibberellic acid mediated signaling pathway / gibberellic acid mediated signaling pathway / response to abscisic acid / cellular response to phosphate starvation / sequence-specific DNA binding / DNA-binding transcription factor activity / regulation of transcription by RNA polymerase II / regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / DNA-templated transcription / nucleus
Similarity search - Function
Transcriptional factor DELLA, N-terminal / DELLA, N-terminal domain superfamily / Transcriptional regulator DELLA protein N terminal / Transcriptional regulator DELLA protein N terminal / Transcription factor GRAS / GRAS domain family / GRAS family profile.
Similarity search - Domain/homology
Biological speciesMedicago truncatula (barrel medic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsWan, L.H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32000900 China
CitationJournal: Nat Commun / Year: 2026
Title: Structure-guided reprogramming of DELLA turnover for a sustainable Green Revolution in rice.
Authors: Chongyu Xue / Shuang Zhang / Lihao Wan / Zhihui Zhang / Chenchen Zhang / Huangqi Chen / Kai Peng / Yujie Wang / Jie Hu / Xiuhua Gao / Jiamu Du / Xiangdong Fu / Shutong Xu /
Abstract: The Green Revolution of the 1960s significantly boosted cereal yields but incurred substantial environmental costs due to overreliance on chemical fertilizer inputs; thus, future agricultural ...The Green Revolution of the 1960s significantly boosted cereal yields but incurred substantial environmental costs due to overreliance on chemical fertilizer inputs; thus, future agricultural sustainability demands improved nitrogen-use efficiency (NUE). The semi-dwarf Green Revolution varieties (GRVs) characterized by elevated DELLA protein accumulation introduce a fundamental trade-off, increasing lodging resistance and harvest index at the expense of diminished biomass and grain productivity per plant, and require high nitrogen fertilizer inputs to achieve maximum yield potential under high planting density. Here we show that gibberellin (GA)-bound GA-INSENSITIVE DWARF1 (GID1) induces multi-level conformational changes in DELLA protein, affecting its N-terminal DELLA and VHYN/DPT/S and C-terminal VVLV and SAW motifs, thereby facilitating recognition by the SKP1-CULLIN-F-box (SCF) ubiquitin ligase complex and subsequent proteasomal degradation. We also performed structure-guided engineering of the rice SLENDER RICE1 (SLR1)-GID1-GID2 complex and created a series of dwarf alleles exhibiting a continuous spectrum of plant heights in elite cultivars. Notably, the dominant alleles slr1 and slr1 achieved superior yield and enhanced NUE over conventional sd1-containing GRVs. Reprogramming DELLA turnover thus enables to break the long-standing trade-off between high yield and fertilizer dependency, offering a strategy toward a more sustainable and productive Green Revolution.
History
DepositionOct 13, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 8, 2026Provider: repository / Type: Initial release
Revision 1.1Aug 19, 2026Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DELLA protein 1
B: DELLA protein 1
C: DELLA protein 1


Theoretical massNumber of molelcules
Total (without water)127,4043
Polymers127,4043
Non-polymers00
Water10,971609
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Exists as a monomer in solution
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6260 Å2
ΔGint-52 kcal/mol
Surface area41870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.441, 91.441, 229.079
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z

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Components

#1: Protein DELLA protein 1 / MtDELLA1


Mass: 42467.988 Da / Num. of mol.: 3 / Mutation: C386S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Medicago truncatula (barrel medic) / Gene: DELLA1, MTR_3g065980, MtrunA17_Chr3g0110971 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A396IUP1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 609 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.17 Å3/Da / Density % sol: 43.32 %
Crystal growTemperature: 289.15 K / Method: evaporation
Details: 0.1 M HEPES pH 8.1, 0.05 M MgCl2, and 30% (v/v) PEG400
PH range: 8.1

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 1.07066 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 5, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07066 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 76178 / % possible obs: 100 % / Redundancy: 18.1 % / Biso Wilson estimate: 23.56 Å2 / CC1/2: 0.99 / Net I/σ(I): 38.8
Reflection shellResolution: 2→2.07 Å / Num. unique obs: 6396 / CC1/2: 0.93

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.20.1_4487phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→38.18 Å / SU ML: 0.1604 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.747
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2088 3553 4.78 %
Rwork0.1808 70826 -
obs0.1821 74379 97.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.52 Å2
Refinement stepCycle: LAST / Resolution: 2→38.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8193 0 0 609 8802
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00628374
X-RAY DIFFRACTIONf_angle_d0.782311338
X-RAY DIFFRACTIONf_chiral_restr0.0491269
X-RAY DIFFRACTIONf_plane_restr0.00491460
X-RAY DIFFRACTIONf_dihedral_angle_d14.70633024
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.030.22611210.21782291X-RAY DIFFRACTION80.53
2.03-2.050.22131220.19992450X-RAY DIFFRACTION85.73
2.05-2.080.28281320.24382567X-RAY DIFFRACTION89.43
2.08-2.120.22731400.20812660X-RAY DIFFRACTION94.12
2.12-2.150.27011330.19962784X-RAY DIFFRACTION97.75
2.15-2.190.20361370.19822856X-RAY DIFFRACTION98.75
2.19-2.230.23531350.19522872X-RAY DIFFRACTION99.5
2.23-2.270.31721330.27432756X-RAY DIFFRACTION96.53
2.27-2.320.21481540.19132844X-RAY DIFFRACTION100
2.32-2.370.23461490.18482876X-RAY DIFFRACTION100
2.37-2.420.19491560.18332879X-RAY DIFFRACTION99.97
2.42-2.480.2071390.17742888X-RAY DIFFRACTION100
2.48-2.550.20571260.17382907X-RAY DIFFRACTION100
2.55-2.630.21681380.18292886X-RAY DIFFRACTION100
2.63-2.710.21331620.18662858X-RAY DIFFRACTION100
2.71-2.810.26541810.19162840X-RAY DIFFRACTION100
2.81-2.920.23531640.19022875X-RAY DIFFRACTION99.97
2.92-3.050.2181570.17752921X-RAY DIFFRACTION99.97
3.05-3.210.20561350.17922876X-RAY DIFFRACTION99.97
3.21-3.420.18911370.1792937X-RAY DIFFRACTION99.93
3.42-3.680.17491240.15832961X-RAY DIFFRACTION100
3.68-4.050.18231280.15752945X-RAY DIFFRACTION99.97
4.05-4.630.16661420.15022964X-RAY DIFFRACTION100
4.63-5.830.21741470.17583002X-RAY DIFFRACTION100
5.84-38.180.17981610.18313131X-RAY DIFFRACTION99.46
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)
14.74263098785-1.464648500491.149350497380.934128009957-0.5498445847590.778391390932-0.0938579548869-0.455259112543-0.4030861210250.06650748409590.115269789475-0.05455850581390.06107433332390.021494237965-0.00395122662760.208154916203-0.01908486602530.03574132981690.2708552441730.03784912273020.219311822985-92.74613039215.0403449599923.5460087167
24.16228014487-1.41225410628-0.4385928054675.385135293840.3724767020051.792146476530.0320868667716-0.348266959897-0.2542864274960.1587091053090.09122996427580.2514605697290.133797595078-0.105625774038-0.1071033715080.147582332555-0.05913904332410.006247786816350.2361968445040.03299902920760.14594186622-119.3254552239.2385098629918.5769231785
33.16040881449-0.6486973546331.217118761882.09285557696-0.630788986621.951178334970.015366855867-0.0227148051952-0.200904041284-0.1522269030060.0170169984474-0.04124259226660.12516938401-0.0682977415708-0.01634573217520.138119570364-0.03761369782760.05120051023820.147318777381-0.01266122443850.113312278968-100.1521260396.3819167454312.3554714264
44.916533539850.1008064502611.7811903163.60205977249-0.2002968562581.96915966494-0.08413321754810.06581393704550.3852106177670.0108484166460.0679862091093-0.291822768993-0.1598988959850.1903824751460.02392161937130.129925028899-0.03534381372480.05778732462610.163487098512-0.005162489977560.181084541319-98.901093565422.24286044713.3713486641
50.4795994126530.6988613317120.1789643729042.749858860850.6186798464350.755553515257-0.0385384559675-0.1886188179730.6433071142621.00414443237-0.4033839463581.63655645204-0.185879369555-0.29584848072-0.1908618385750.612135230666-0.1334811900550.4487965033650.436102166343-0.1019124930351.16268070665-117.31372308333.547582151621.9860773912
61.103977749631.008654214010.0527678282061.94720949570.00289166232610.4556586962310.0314964879169-0.4695004239990.04307190985930.823454474421-0.2115377428570.990427453513-0.0314210311029-0.196992917954-0.1313569187470.5469450661070.03293414081880.3431726770580.3475969317030.02195153971060.542739961121-103.6813640847.068038417328.3292246256
71.13151496756-0.08324084662160.3848956892124.288910420590.154580005271.56064310297-0.159032587388-0.0732968907050.05750582749330.2691875987580.146335488369-0.168180856685-0.03264053939590.0972730827692-0.008336265805240.1799634766990.0151438387369-0.007899237424420.121007738177-0.01421283954010.103427305319-82.784042213760.673209328519.0139239057
87.942947227011.034334145971.720503028933.747461878081.97105591393.32275136252-0.121283558653-0.3083105094940.4267544333950.082951469208-0.06124620413280.281793788117-0.301629861680.02805678386490.1574692663490.3060393723790.02325285059690.02305354805340.121743202954-0.006578036819560.190172035186-87.250984852768.586464523921.9488332073
92.250204789960.715068716633-0.5887016033614.13312023004-0.3618238360341.23285917473-0.09334279950870.09244804020120.0865954935185-0.1805805009530.05642291744940.497463632786-0.0949694146115-0.06040036711350.04395154268590.1833101012520.0170963563887-0.01146718359050.123348456141-0.02735470189770.128567365461-95.647356413853.342111625811.0302702292
102.982789590650.160932775224-0.5155884484472.94546647811-0.1366723598712.210217301020.0327509231826-0.148804965074-0.00432437130080.226362695396-0.01781015321770.570023792954-0.101111324349-0.0734099393536-0.03885835581510.198290570380.03004250061480.05055767457770.0956355125679-0.03414809573430.214786076158-98.504031976648.467908968714.2348105686
113.06168766666-0.2993106965610.136436903063.73491944978-0.8466779111362.660027222680.0259191608882-0.0231312309996-0.3544378638550.082640936913-0.0140245327573-0.2106450066340.2039366864640.1582309352330.00820438466320.1724125646780.0308522620777-0.007478829051060.113768133456-0.02632283839810.16032300276-83.419152588442.286403244614.6555897059
125.564478096652.268981383610.2783682451275.50840247683-0.05532887922453.55518153652-0.407856363473-0.7105134004841.034685801310.5760167054550.308404437269-0.810518511621-0.2224886523720.1894527698670.05738122053590.4410152791520.139043600805-0.2060309166070.318300678751-0.1363413822020.672724577988-66.088887878851.92791974125.8714310741
133.77778984854.11734821491-0.196916611596.65469708694-1.554405716415.11640293801-0.0962755503489-0.5056625244190.5282127006450.9264784623490.100916144219-0.704252486541-0.0942737794248-0.111033095814-0.01570406080740.4126097195820.143395109862-0.1850682949820.344465527474-0.2219496917610.562888372832-62.255876121343.280424362929.2875676945
146.528324216961.924033862352.262730516528.480634172541.260892781295.829355909610.155685340913-0.5695829095660.1847067713141.043415462870.134266574924-0.657976887909-0.01842511019740.578640125369-0.2529559501170.4199126920720.119980504896-0.03880615242250.493508874814-0.1132800597870.294675585331-58.999928955924.507850964532.5862059913
155.05338828942-1.79423344713-1.577961279036.935399722353.091507254955.06153564192-0.153673909326-0.0780444815195-0.377895893557-0.00208842416118-0.08476172021120.363566378360.122193862595-0.3328533933260.2130501686710.1265250465790.01359284959540.01298533152150.1259686602910.07041473519440.114023451364-63.64127096788.8420946750517.7649137784
162.660642805850.534620961445-0.7752424791784.55574262606-1.326122447992.21963493685-0.0741623264806-0.595587555083-0.3414150711220.290177143465-0.071170201693-0.4412746963670.04344589184510.2738204268720.1110833414590.1715662003490.0582388678149-0.004771159083960.2860009953040.05030225866070.189144071663-53.47823348357.965755728224.8313383951
172.40686031917-1.81215745546-0.4823848467284.040210583131.53303514211.20728052577-0.0826864419160.01222306528380.194293724406-0.01079456382580.110785890696-0.2890678083530.01401742048310.0678660553276-0.02967966368440.09741564959190.01306908397-0.004050660509720.158331323880.02312827172020.113676679631-58.009182575723.586620456114.2384904868
181.98578267952-0.932574029847-0.5538293661413.10585117391-0.151920298335.90827868124-0.0619809441854-0.4157461972950.3948517839750.3708087546970.0259076022992-0.406643563976-0.2804580326880.01549023056750.0230965418120.1512155794740.0383736598227-0.06384590194310.239684910109-0.06755381605980.290393692015-59.159417678833.648652857824.2348314285
193.212334938110.517372709597-1.143612993712.540024780270.1221114650021.99187509374-0.09065931972840.2831302182720.0138585200293-0.456988829158-0.0943548377680.210375892955-0.135942259768-0.294645006274-0.04059060649850.1549531038170.00592204984204-0.01154603647480.2566016795540.0133802219840.128167814301-63.718436489520.42251782564.81700563693
203.35088687652-0.178811020459-0.3242662558052.954260637780.4660303002281.99132786959-0.1019317819250.01031968770250.0463148793590.07450019154780.05757145627930.358926436520.0402454312227-0.2304545716530.06854176032510.1097393118670.017081381122-0.01454102857390.2109503865350.04214311698540.180069725559-73.013111280617.932199691514.6216086266
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 211 through 319 )AA211 - 3191 - 104
22chain 'A' and (resid 320 through 393 )AA320 - 393105 - 178
33chain 'A' and (resid 394 through 541 )AA394 - 541179 - 308
44chain 'A' and (resid 542 through 589 )AA542 - 589309 - 352
55chain 'B' and (resid 211 through 249 )BB211 - 2491 - 39
66chain 'B' and (resid 250 through 292 )BB250 - 29240 - 76
77chain 'B' and (resid 293 through 359 )BB293 - 35977 - 143
88chain 'B' and (resid 360 through 393 )BB360 - 393144 - 177
99chain 'B' and (resid 394 through 470 )BB394 - 470178 - 254
1010chain 'B' and (resid 471 through 541 )BB471 - 541255 - 303
1111chain 'B' and (resid 542 through 589 )BB542 - 589304 - 347
1212chain 'C' and (resid 210 through 249 )CC210 - 2491 - 40
1313chain 'C' and (resid 250 through 268 )CC250 - 26841 - 59
1414chain 'C' and (resid 269 through 292 )CC269 - 29260 - 78
1515chain 'C' and (resid 293 through 319 )CC293 - 31979 - 105
1616chain 'C' and (resid 320 through 393 )CC320 - 393106 - 179
1717chain 'C' and (resid 394 through 470 )CC394 - 470180 - 256
1818chain 'C' and (resid 471 through 522 )CC471 - 522257 - 286
1919chain 'C' and (resid 523 through 541 )CC523 - 541287 - 305
2020chain 'C' and (resid 542 through 591 )CC542 - 591306 - 351

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