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- PDB-5ryz: EPB41L3 PanDDA analysis group deposition -- Crystal Structure of ... -

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Basic information

Entry
Database: PDB / ID: 5ryz
TitleEPB41L3 PanDDA analysis group deposition -- Crystal Structure of the FERM domain of human EPB41L3 in complex with Z2856434868
ComponentsIsoform 2 of Band 4.1-like protein 3
KeywordsCELL ADHESION / SGC - Diamond I04-1 fragment screening / PanDDA / XChemExplorer
Function / homology
Function and homology information


protein localization to paranode region of axon / cytoskeletal protein-membrane anchor activity / paranodal junction assembly / protein localization to juxtaparanode region of axon / myelin maintenance / paranode region of axon / cortical cytoskeleton organization / actomyosin structure organization / juxtaparanode region of axon / Neurexins and neuroligins ...protein localization to paranode region of axon / cytoskeletal protein-membrane anchor activity / paranodal junction assembly / protein localization to juxtaparanode region of axon / myelin maintenance / paranode region of axon / cortical cytoskeleton organization / actomyosin structure organization / juxtaparanode region of axon / Neurexins and neuroligins / Sensory processing of sound by outer hair cells of the cochlea / Sensory processing of sound by inner hair cells of the cochlea / cortical actin cytoskeleton organization / neuron projection morphogenesis / protein localization to plasma membrane / structural constituent of cytoskeleton / cell-cell junction / cell junction / regulation of cell shape / actin binding / cytoskeleton / apoptotic process / plasma membrane / cytosol
Similarity search - Function
Band 4.1-like protein 3 / SAB domain / Band 4.1, C-terminal / SAB domain / 4.1 protein C-terminal domain (CTD) / FERM adjacent (FA) / FERM adjacent (FA) / FERM adjacent (FA) / Ezrin/radixin/moesin-like / FERM, C-terminal PH-like domain ...Band 4.1-like protein 3 / SAB domain / Band 4.1, C-terminal / SAB domain / 4.1 protein C-terminal domain (CTD) / FERM adjacent (FA) / FERM adjacent (FA) / FERM adjacent (FA) / Ezrin/radixin/moesin-like / FERM, C-terminal PH-like domain / FERM C-terminal PH-like domain / FERM C-terminal PH-like domain / FERM, N-terminal / FERM N-terminal domain / FERM domain signature 1. / FERM conserved site / FERM domain signature 2. / FERM central domain / FERM/acyl-CoA-binding protein superfamily / FERM central domain / FERM superfamily, second domain / FERM domain / FERM domain profile. / Band 4.1 domain / Band 4.1 homologues / PH-like domain superfamily / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
1-ethyl-N-(2-fluorophenyl)piperidin-4-amine / Band 4.1-like protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / molecular replacement / Resolution: 1.61 Å
AuthorsBradshaw, W.J. / Katis, V.L. / Newman, J.A. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Gileadi, O.
CitationJournal: To Be Published
Title: EPB41L3 PanDDA analysis group deposition
Authors: Bradshaw, W.J. / Katis, V.L. / Newman, J.A. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Gileadi, O.
History
DepositionOct 30, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 11, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Isoform 2 of Band 4.1-like protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0689
Polymers33,3951
Non-polymers6738
Water2,810156
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.530, 77.550, 99.520
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Isoform 2 of Band 4.1-like protein 3 / 4.1B / Differentially expressed in adenocarcinoma of the lung protein 1 / DAL-1 / Erythrocyte ...4.1B / Differentially expressed in adenocarcinoma of the lung protein 1 / DAL-1 / Erythrocyte membrane protein band 4.1-like 3


Mass: 33395.305 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EPB41L3, DAL1, KIAA0987 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y2J2
#2: Chemical ChemComp-NVY / 1-ethyl-N-(2-fluorophenyl)piperidin-4-amine


Mass: 222.302 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H19FN2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 156 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.23 Å3/Da / Density % sol: 44.75 % / Mosaicity: 0 °
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.075M ammonium nitrate, 0.1M MES pH 6.0, 6.5% PEG 2000, 6.5% PEG 3350, 6.5% PEG 4000, 6.5% PEG 5000, 10% ethylene glycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91587 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 12, 2019
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91587 Å / Relative weight: 1
ReflectionResolution: 1.61→61.17 Å / Num. obs: 39479 / % possible obs: 99.9 % / Redundancy: 6.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.033 / Rrim(I) all: 0.082 / Net I/σ(I): 12.1 / Num. measured all: 244600 / Scaling rejects: 9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.61-1.655.21.4041465928410.4880.6841.5671.199.9
7.2-61.175.50.03528955310.9980.0160.0393899.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0238refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.23data extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 6IBE

6ibe


Resolution: 1.61→61.17 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.939 / SU B: 2.995 / SU ML: 0.098 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.129 / ESU R Free: 0.12 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2436 1962 5 %RANDOM
Rwork0.2106 ---
obs0.2122 37453 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 77.59 Å2 / Biso mean: 32.174 Å2 / Biso min: 14.92 Å2
Baniso -1Baniso -2Baniso -3
1--0.39 Å20 Å20 Å2
2--1.23 Å2-0 Å2
3----0.84 Å2
Refinement stepCycle: final / Resolution: 1.61→61.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2335 0 44 156 2535
Biso mean--41.52 32.2 -
Num. residues----284
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0143719
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173021
X-RAY DIFFRACTIONr_angle_refined_deg1.5321.6634456
X-RAY DIFFRACTIONr_angle_other_deg1.3541.6027028
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2395409
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.3620.657198
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.7715588
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5821533
X-RAY DIFFRACTIONr_chiral_restr0.0780.2397
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023878
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02785
X-RAY DIFFRACTIONr_mcbond_it2.3433.3731762
X-RAY DIFFRACTIONr_mcbond_other2.3553.3691744
X-RAY DIFFRACTIONr_mcangle_it3.8844.7841989
LS refinement shellResolution: 1.61→1.652 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 127 -
Rwork0.328 2709 -
all-2836 -
obs--99.86 %

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