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- PDB-9f2m: To be published -

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Basic information

Entry
Database: PDB / ID: 9f2m
TitleTo be published
Components
  • Autophagy-related protein
  • RxLR effector protein 54
KeywordsPEPTIDE BINDING PROTEIN / SIGNALING PROTEIN Autophagy related protein
Function / homology
Function and homology information


phosphatidylethanolamine binding / cellular response to nitrogen starvation / autophagosome membrane / autophagosome assembly / autophagosome maturation / mitophagy / host cell cytoplasm / host cell nucleus / extracellular region
Similarity search - Function
RXLR phytopathogen effector protein, WY-domain / RXLR phytopathogen effector protein WY-domain / : / Effector PexRD54, WY-domain / Autophagy protein Atg8 ubiquitin-like / Autophagy protein Atg8 ubiquitin like / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Autophagy-related protein / RxLR effector protein 54
Similarity search - Component
Biological speciesMarchantia polymorpha (liverwort)
Phytophthora infestans (potato late blight agent)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsSanchez de Medina, V. / Dagdas, Y.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)101000981European Union
CitationJournal: To Be Published
Title: To be published
Authors: Nn, N. / Pp, P.
History
DepositionApr 23, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 21, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Autophagy-related protein
D: RxLR effector protein 54


Theoretical massNumber of molelcules
Total (without water)13,3102
Polymers13,3102
Non-polymers00
Water1,63991
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area830 Å2
ΔGint-5 kcal/mol
Surface area7170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.230, 36.230, 69.590
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32
Space group name HallP32
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3

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Components

#1: Protein Autophagy-related protein


Mass: 12649.649 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: N- and C-terminal truncated variant / Source: (gene. exp.) Marchantia polymorpha (liverwort) / Gene: MARPO_0001s0494 / Production host: Escherichia coli B (bacteria) / References: UniProt: A0A2R6XWU1
#2: Protein/peptide RxLR effector protein 54


Mass: 660.715 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Peptide from Irish potato famine pathogen effector protein PexRD54
Source: (synth.) Phytophthora infestans (potato late blight agent)
References: UniProt: D0NBE6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / 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: 1.98 Å3/Da / Density % sol: 37.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 25% (w/v) PEG 1500, 100 mM PCTP (sodium propionic acid, sodium cacodylate, Bis-Tris propane) pH 5.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54789 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 11, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54789 Å / Relative weight: 1
ReflectionResolution: 1.75→30 Å / Num. obs: 10224 / % possible obs: 98.5 % / Redundancy: 3.4 % / Biso Wilson estimate: 28.93 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.037 / Net I/σ(I): 23.1
Reflection shellResolution: 1.75→1.85 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 5.4 / Num. unique obs: 1643 / CC1/2: 0.964 / Rrim(I) all: 0.224 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→28.6 Å / SU ML: 0.2553 / Cross valid method: FREE R-VALUE / σ(F): 2.01 / Phase error: 29.4391
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2402 511 5 %
Rwork0.192 9707 -
obs0.1945 10218 98.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.05 Å2
Refinement stepCycle: LAST / Resolution: 1.75→28.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms938 0 0 91 1029
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0149991
X-RAY DIFFRACTIONf_angle_d1.36381344
X-RAY DIFFRACTIONf_chiral_restr0.0944148
X-RAY DIFFRACTIONf_plane_restr0.0149172
X-RAY DIFFRACTIONf_dihedral_angle_d13.879392
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.920.33541280.25422447X-RAY DIFFRACTION99.61
1.92-2.20.25481270.21912409X-RAY DIFFRACTION99.1
2.2-2.770.28121310.22892488X-RAY DIFFRACTION99.54
2.77-28.60.21071250.16352363X-RAY DIFFRACTION96.21
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)
11.60820574873-0.209133425622-1.385117407823.862230019510.1347325783753.733789093120.1374506815920.299671316343-0.273245732396-0.0351327174408-0.234772241640.06032018751710.1298866462190.05761996196890.09477082025710.2250901843150.000157393399053-0.07903080238390.365516304614-0.03476897244790.275623878359-15.3262743667-2.14453377671-25.944126978
23.954128093180.02703665069550.2740054264192.181302579390.6528791797513.371653105110.1153966254010.2397629657630.1200772394180.084339471152-0.1936279199350.150386527276-0.4213573876310.04711861114160.08918438343610.282141851675-0.03864920048460.005401468131080.2350596418270.02619336261010.207215641547-23.65125460366.64492298478-17.551923218
32.037775094970.020806310253-0.4951244227654.08454095527-0.2815177690052.148755357450.26251272901-0.274352814867-0.2719026584530.407826575834-0.215098133692-0.1713726680190.01382108817260.35875483475-0.01792868154260.256614319486-0.0499725944112-0.06972656380150.3580307023210.04368902502290.317470627531-14.4727875784-1.46697333079-17.5059529366
45.661723199950.8556798839461.274819435433.387802646274.572007104736.219587071530.4685753224370.850181568095-0.289684534235-0.6764395825610.0160565728759-0.4178572823870.12640711385-0.941064508564-0.6116114816540.368523444003-0.06038569910450.04379403875640.5011213241920.06201288092990.244233920585-14.21097879424.82912173856-31.6310491709
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 5 through 57 )AA5 - 571 - 53
22chain 'A' and (resid 58 through 91 )AA58 - 9154 - 87
33chain 'A' and (resid 92 through 113 )AA92 - 11388 - 109
44chain 'D' and (resid 1 through 5 )DB1 - 51 - 5

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