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- PDB-9drw: Myocilin OLF mutant A427T -

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Basic information

Entry
Database: PDB / ID: 9drw
TitleMyocilin OLF mutant A427T
ComponentsMyocilin
KeywordsCELL ADHESION / olfactomedin
Function / homology
Function and homology information


skeletal muscle hypertrophy / clustering of voltage-gated sodium channels / myosin light chain binding / non-canonical Wnt signaling pathway / myelination in peripheral nervous system / frizzled binding / node of Ranvier / negative regulation of stress fiber assembly / negative regulation of Rho protein signal transduction / positive regulation of mitochondrial depolarization ...skeletal muscle hypertrophy / clustering of voltage-gated sodium channels / myosin light chain binding / non-canonical Wnt signaling pathway / myelination in peripheral nervous system / frizzled binding / node of Ranvier / negative regulation of stress fiber assembly / negative regulation of Rho protein signal transduction / positive regulation of mitochondrial depolarization / ERBB2-ERBB3 signaling pathway / regulation of MAPK cascade / fibronectin binding / negative regulation of cell-matrix adhesion / positive regulation of focal adhesion assembly / rough endoplasmic reticulum / positive regulation of stress fiber assembly / positive regulation of substrate adhesion-dependent cell spreading / positive regulation of JNK cascade / bone development / receptor tyrosine kinase binding / mitochondrial intermembrane space / neuron projection development / osteoblast differentiation / : / cytoplasmic vesicle / mitochondrial outer membrane / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / mitochondrial inner membrane / cilium / positive regulation of cell migration / endoplasmic reticulum / Golgi apparatus / signal transduction / extracellular space / extracellular exosome / metal ion binding
Similarity search - Function
: / Olfactomedin-like domain / Olfactomedin-like domain / Olfactomedin-like domain profile. / Olfactomedin-like domains
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsScelsi, H.F. / Lieberman, R.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Eye Institute (NIH/NEI)R01EY021205 United States
CitationJournal: To Be Published
Title: Structural basis for anomalous cellular trafficking behavior of glaucoma-associated A427T mutant myocilin
Authors: Scelsi, H.F. / Lieberman, R.L.
History
DepositionSep 26, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 3, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Myocilin
B: Myocilin
C: Myocilin
D: Myocilin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,25213
Polymers124,9084
Non-polymers3449
Water13,673759
1
A: Myocilin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2903
Polymers31,2271
Non-polymers632
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Myocilin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3824
Polymers31,2271
Non-polymers1553
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Myocilin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2903
Polymers31,2271
Non-polymers632
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Myocilin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2903
Polymers31,2271
Non-polymers632
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)140.930, 47.810, 149.990
Angle α, β, γ (deg.)90.000, 107.710, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein
Myocilin / Myocilin 55 kDa subunit / Trabecular meshwork-induced glucocorticoid response protein


Mass: 31227.008 Da / Num. of mol.: 4 / Mutation: A427T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MYOC, GLC1A, TIGR / Plasmid: pMAL-c4x / Production host: Escherichia coli (E. coli) / References: UniProt: Q99972
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 759 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 1.93 Å3/Da / Density % sol: 36.24 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.2 / Details: 10% PEG8000, 0.05M magnesium chloride

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Nov 2, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.45→58.62 Å / Num. obs: 160850 / % possible obs: 95.06 % / Redundancy: 6.7 % / Biso Wilson estimate: 14.69 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.06408 / Rpim(I) all: 0.02663 / Rrim(I) all: 0.06952 / Net I/σ(I): 16.18
Reflection shellResolution: 1.45→1.502 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.5379 / Mean I/σ(I) obs: 4.45 / Num. unique obs: 12829 / CC1/2: 0.912 / CC star: 0.977 / Rpim(I) all: 0.2414 / Rrim(I) all: 0.5928 / % possible all: 76.52

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.45→58.62 Å / SU ML: 0.1514 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.0321
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1882 3883 1.24 %
Rwork0.1457 308789 -
obs0.1462 160850 94.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.16 Å2
Refinement stepCycle: LAST / Resolution: 1.45→58.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8154 0 14 759 8927
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00448590
X-RAY DIFFRACTIONf_angle_d0.806111762
X-RAY DIFFRACTIONf_chiral_restr0.08161307
X-RAY DIFFRACTIONf_plane_restr0.00441498
X-RAY DIFFRACTIONf_dihedral_angle_d12.30431182
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.470.2904970.24087804X-RAY DIFFRACTION67.33
1.47-1.490.33841130.21588850X-RAY DIFFRACTION75.26
1.49-1.510.23231230.19229967X-RAY DIFFRACTION86.22
1.51-1.530.27271380.173110648X-RAY DIFFRACTION91.31
1.53-1.550.22651420.161710989X-RAY DIFFRACTION92.82
1.55-1.570.21471330.145110923X-RAY DIFFRACTION95.06
1.57-1.60.23591420.141811282X-RAY DIFFRACTION96.27
1.6-1.620.20631420.139911286X-RAY DIFFRACTION96.42
1.62-1.650.12961400.135611353X-RAY DIFFRACTION96.6
1.65-1.680.17921420.134111118X-RAY DIFFRACTION96.63
1.68-1.710.19451440.131411346X-RAY DIFFRACTION96.9
1.71-1.750.22521410.141311234X-RAY DIFFRACTION96.96
1.75-1.790.23021430.136911369X-RAY DIFFRACTION97.06
1.79-1.830.21141450.137111383X-RAY DIFFRACTION97.24
1.83-1.870.23321450.131311264X-RAY DIFFRACTION97.29
1.87-1.920.18431430.134811333X-RAY DIFFRACTION97.38
1.92-1.980.22431430.13611438X-RAY DIFFRACTION97.27
1.98-2.040.2061410.138811291X-RAY DIFFRACTION97
2.04-2.120.18291420.142211276X-RAY DIFFRACTION97.15
2.12-2.20.18411390.139711376X-RAY DIFFRACTION97.03
2.2-2.30.1751450.143611388X-RAY DIFFRACTION97.94
2.3-2.420.22581420.144411417X-RAY DIFFRACTION97.97
2.42-2.570.1961460.157411490X-RAY DIFFRACTION98.03
2.57-2.770.18931450.162811452X-RAY DIFFRACTION98.36
2.77-3.050.17641420.1611395X-RAY DIFFRACTION98
3.05-3.490.17721390.147511405X-RAY DIFFRACTION97.41
3.49-4.40.14481410.127611217X-RAY DIFFRACTION96.17
4.4-58.620.16871450.146311495X-RAY DIFFRACTION98.56

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