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- PDB-7bvw: Crystal structure of the RING-H2 domain of Arabidopsis RMR1 -

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Basic information

Entry
Database: PDB / ID: 7bvw
TitleCrystal structure of the RING-H2 domain of Arabidopsis RMR1
ComponentsAT5G66160 protein
KeywordsTRANSPORT PROTEIN / C3H2C3 / ring finger / E3 ligase
Function / homology: / Ring finger domain / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type / membrane / AT5G66160 protein
Function and homology information
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsChen, S. / Wong, K.B.
CitationJournal: J.Biol.Chem. / Year: 2025
Title: The RING-finger domain of Arabidopsis RMR functions as an E3 ligase essential for post-Golgi trafficking.
Authors: Chen, S. / Zeng, Y.L. / Wong, H.Y. / Chen, Y.H. / Yang, L. / Luo, F. / Gao, C.J. / Jiang, L.W. / Wong, K.B.
History
DepositionApr 12, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 14, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Sep 24, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: AT5G66160 protein
B: AT5G66160 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7918
Polymers18,4412
Non-polymers3506
Water1,31573
1
A: AT5G66160 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,4174
Polymers9,2211
Non-polymers1963
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5090 Å2
MethodPISA
2
B: AT5G66160 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,3744
Polymers9,2211
Non-polymers1543
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-11 kcal/mol
Surface area4790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.431, 23.648, 75.699
Angle α, β, γ (deg.)90.000, 94.800, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-403-

ZN

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Components

#1: Protein AT5G66160 protein / Really-Interesting-New-Gene (RING) domain


Mass: 9220.559 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At5g66160 / Production host: Escherichia coli (E. coli) / Strain (production host): SoluBL21 / References: UniProt: C0Z2X4
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 1.8 Å3/Da / Density % sol: 31.67 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.2 M Ammonium acetate, 0.1 M BIS-TRIS pH 5.5, 20% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jan 4, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.1→37.72 Å / Num. obs: 7849 / % possible obs: 98.5 % / Redundancy: 3.6 % / CC1/2: 0.992 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.061 / Rrim(I) all: 0.116 / Net I/σ(I): 9 / Num. measured all: 27884
Reflection shellResolution: 2.1→2.16 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.213 / Num. unique obs: 650 / CC1/2: 0.95 / Rpim(I) all: 0.135 / Rrim(I) all: 0.253 / % possible all: 97.4

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4V3K

4v3k


Resolution: 2.1→32.23 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 25.31
RfactorNum. reflection% reflection
Rfree0.2219 422 5.38 %
Rwork0.1791 --
obs0.1815 7846 97.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 87.05 Å2 / Biso mean: 27.392 Å2 / Biso min: 12.33 Å2
Refinement stepCycle: final / Resolution: 2.1→32.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1184 0 6 73 1263
Biso mean--24.23 32.65 -
Num. residues----154
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.1-2.40.2721440.1955241197
2.4-3.030.24781140.2042249498
Refinement TLS params.Method: refined / Origin x: 1.4047 Å / Origin y: 5.8871 Å / Origin z: 94.4639 Å
111213212223313233
T0.1217 Å2-0.0052 Å20.0021 Å2-0.1062 Å2-0.0178 Å2--0.2148 Å2
L3.8357 °21.6406 °20.4386 °2-1.5369 °20.0277 °2--0.3544 °2
S0.0314 Å °-0.0805 Å °-0.0116 Å °0.0639 Å °-0.0459 Å °0.0266 Å °-0.029 Å °0.0012 Å °0.0052 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA205 - 402
2X-RAY DIFFRACTION1allA501
3X-RAY DIFFRACTION1allB205 - 279
4X-RAY DIFFRACTION1allB401 - 501
5X-RAY DIFFRACTION1allS1 - 76

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