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- EMDB-64837: the open state of NAL1 from indica with R233H -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-64837
Titlethe open state of NAL1 from indica with R233H
Map data
Sample
  • Complex: Narrow leaf 1 (NAL1) from Indica with R233H mutantion
    • Other: The open state of narrow leaf 1 from Indica with R233H mutanti0n
Keywordsa single piont mutant / close state / rice / india / hexamer / PLANT PROTEIN
Biological speciesOryza sativa Indica Group (long-grained rice)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.6 Å
AuthorsLiu HL / Zhang SJ / Liu CM
Funding support China, 1 items
OrganizationGrant numberCountry
Chinese Academy of Sciences China
CitationJournal: To Be Published
Title: The open state of the R233H isoform of the Indica-type Narrow-leaf gene 1 (NAL1) mutant
Authors: Liu HL / Zhang SJ
History
DepositionMay 29, 2025-
Header (metadata) releaseJun 3, 2026-
Map releaseJun 3, 2026-
UpdateJun 3, 2026-
Current statusJun 3, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_64837.png

Downloads & links

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Map

FileDownload / File: emd_64837.map.gz / Format: CCP4 / Size: 12.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.42 Å/pix.
x 150 pix.
= 213. Å		1.42 Å/pix.
x 150 pix.
= 213. Å		1.42 Å/pix.
x 150 pix.
= 213. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.42 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.143
Minimum - Maximum-0.74428946 - 1.0609889
Average (Standard dev.)0.00091222994 (±0.048580915)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions150150150
Spacing150150150
CellA=B=C: 213.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_64837_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_64837_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Narrow leaf 1 (NAL1) from Indica with R233H mutantion

EntireName: Narrow leaf 1 (NAL1) from Indica with R233H mutantion
Components
  • Complex: Narrow leaf 1 (NAL1) from Indica with R233H mutantion
    • Other: The open state of narrow leaf 1 from Indica with R233H mutanti0n

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Supramolecule #1: Narrow leaf 1 (NAL1) from Indica with R233H mutantion

SupramoleculeName: Narrow leaf 1 (NAL1) from Indica with R233H mutantion / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: The open state of narrow leaf 1 from Indica with R233H mutantion
Source (natural)Organism: Oryza sativa Indica Group (long-grained rice)
Molecular weightTheoretical: 380 KDa

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Macromolecule #1: The open state of narrow leaf 1 from Indica with R233H mutanti0n

MacromoleculeName: The open state of narrow leaf 1 from Indica with R233H mutanti0n
type: other / ID: 1 / Details: A NAL1 from Indica containing an R233H mutation / Classification: other
Source (natural)Organism: Oryza sativa Indica Group (long-grained rice)
SequenceString: MKPSDDKAQL SGLAQSEESS LDVDHQSFPC SPSIQPVASG CTHTENSAAY FLWPTSNLQH CAAEGRANYF GNLQKGLLPR HPGRLPKGQQ ANSLLDLMTI RAFHSKILRR FSLGTAVGFR IRKGDLTDIP AILVFVARKV HKKWLNPAQC LPAILEGPGG VWCDVDVVEF ...String:
MKPSDDKAQL SGLAQSEESS LDVDHQSFPC SPSIQPVASG CTHTENSAAY FLWPTSNLQH CAAEGRANYF GNLQKGLLPR HPGRLPKGQQ ANSLLDLMTI RAFHSKILRR FSLGTAVGFR IRKGDLTDIP AILVFVARKV HKKWLNPAQC LPAILEGPGG VWCDVDVVEF SYYGAPAQTP KEQMFSELVD KLCGSDECIG SGSQVASHET FGTLGAIVKR RTGNKQVGFL TNHHVAVDLD YPNQKMFHPL PPNLGPGVYL GAVERATSFI TDDVWYGIYA GTNPETFVRA DGAFIPFADD FDISTVTTVV RGVGDIGDVK VIDLQCPLNS LIGRQVCKVG RSSGHTTGTV MAYALEYNDE KGICFFTDIL VVGENRQTFD LEGDSGSLII LTSQDGEKPR PIGIIWGGTA NRGRLKLTSD HGPENWTSGV DLGRLLDRLE LDIIITNESL QDAVQQQRFA LVAAVTSAVG ESSGAPVAIP EEKVEEIFEP LGIQIQQLPR HDVAASGTEG EEASNTVVNV EEHQFISNFV GMSPVRDDQD APRSITNLNN PSEEELAMSL HLGDREPKRL RSDSGSSLDL EK
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statecell

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 5.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 1188383
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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