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- PDB-4mgx: Crystal structure of human filamin C domains 4-5 and GPIB alpha c... -

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Basic information

Entry
Database: PDB / ID: 4mgx
TitleCrystal structure of human filamin C domains 4-5 and GPIB alpha cytoplasmic domain complex
Components
  • Filamin-C
  • Platelet glycoprotein Ib alpha chain
KeywordsSTRUCTURAL PROTEIN / immunoglobulin like fold / muscle Z disk
Function / homology
Function and homology information


thrombin-activated receptor activity / glycoprotein Ib-IX-V complex / positive regulation of leukocyte tethering or rolling / blood coagulation, intrinsic pathway / Cell-extracellular matrix interactions / Defective F9 activation / Platelet Adhesion to exposed collagen / costamere / positive regulation of platelet activation / sarcomere organization ...thrombin-activated receptor activity / glycoprotein Ib-IX-V complex / positive regulation of leukocyte tethering or rolling / blood coagulation, intrinsic pathway / Cell-extracellular matrix interactions / Defective F9 activation / Platelet Adhesion to exposed collagen / costamere / positive regulation of platelet activation / sarcomere organization / megakaryocyte development / ankyrin binding / GP1b-IX-V activation signalling / intercellular bridge / regulation of blood coagulation / Platelet Aggregation (Plug Formation) / release of sequestered calcium ion into cytosol / fibrinolysis / Intrinsic Pathway of Fibrin Clot Formation / extracellular matrix / cytoskeletal protein binding / sarcolemma / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / cell morphogenesis / Z disc / platelet activation / actin filament binding / blood coagulation / cell surface receptor signaling pathway / cytoskeleton / cell adhesion / external side of plasma membrane / focal adhesion / cell surface / extracellular space / extracellular exosome / membrane / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Filamin family / Filamin/ABP280 repeat / Filamin-type immunoglobulin domains / Filamin/ABP280 repeat / Filamin/ABP280 repeat profile. / Leucine rich repeat N-terminal domain / Filamin/ABP280 repeat-like / Leucine-rich repeat N-terminal domain / Leucine rich repeat N-terminal domain / Actinin-type actin-binding domain signature 1. ...Filamin family / Filamin/ABP280 repeat / Filamin-type immunoglobulin domains / Filamin/ABP280 repeat / Filamin/ABP280 repeat profile. / Leucine rich repeat N-terminal domain / Filamin/ABP280 repeat-like / Leucine-rich repeat N-terminal domain / Leucine rich repeat N-terminal domain / Actinin-type actin-binding domain signature 1. / Actinin-type actin-binding domain signature 2. / Actinin-type actin-binding domain, conserved site / Leucine-rich repeats, bacterial type / Calponin homology domain / Cysteine-rich flanking region, C-terminal / Leucine rich repeat C-terminal domain / Calponin homology (CH) domain / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Immunoglobulin E-set / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Platelet glycoprotein Ib alpha chain / Filamin-C
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.16 Å
AuthorsSethi, R. / Ylanne, J.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: A Novel Structural Unit in the N-terminal Region of Filamins.
Authors: Sethi, R. / Seppala, J. / Tossavainen, H. / Ylilauri, M. / Ruskamo, S. / Pentikainen, O.T. / Pentikainen, U. / Permi, P. / Ylanne, J.
History
DepositionAug 29, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 12, 2014Group: Database references
Revision 1.2Apr 9, 2014Group: Database references
Revision 1.3Sep 20, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Filamin-C
B: Platelet glycoprotein Ib alpha chain


Theoretical massNumber of molelcules
Total (without water)20,8622
Polymers20,8622
Non-polymers00
Water362
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1040 Å2
ΔGint-6 kcal/mol
Surface area9540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.800, 111.800, 59.880
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number95
Space group name H-MP4322

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Components

#1: Protein Filamin-C / FLN-C / FLNc / ABP-280-like protein / ABP-L / Actin-binding-like protein / Filamin-2 / Gamma-filamin


Mass: 19793.359 Da / Num. of mol.: 1 / Fragment: domains 4 and 5 (UNP residues 572-756)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FLNC, ABPL, FLN2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q14315
#2: Protein/peptide Platelet glycoprotein Ib alpha chain / GP-Ib alpha / GPIb-alpha / GPIbA / Glycoprotein Ibalpha / Antigen CD42b-alpha / Glycocalicin


Mass: 1068.246 Da / Num. of mol.: 1 / Fragment: cytoplasmic domain (UNP residues 577-585) / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P07359
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O

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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: 4.48 Å3/Da / Density % sol: 72.57 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M HEPES, pH 7.5, 20% w/v PEG8000, VAPOR DIFFUSION, HANGING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97625 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 3, 2013
RadiationMonochromator: liquid nitrogen cooled channel-cut Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 3→47.73 Å / Num. all: 8069 / Num. obs: 8054 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 9.72 % / Biso Wilson estimate: 87.694 Å2 / Rmerge(I) obs: 0.196 / Rsym value: 0.207 / Net I/σ(I): 8.53
Reflection shell
Resolution (Å)Mean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
3-3.070.292976569198.4
3.07-3.160.543770570199.8
3.16-3.250.7243295481100
3.25-3.351.3354745291100
3.35-3.462.2258935211100
3.46-3.583.2856205071100
3.58-3.724.3154134901100
3.72-3.874.9947264631100
3.87-4.046.0549864581100
4.04-4.248.3648794381100
4.24-4.4711.3144724121100
4.47-4.7414.0340873941100
4.74-5.0615.3639953801100
5.06-5.4717.4737973501100
5.47-5.9917.1334433261100
5.99-6.717.1529382971100
6.7-7.7419.7527552631100
7.74-9.4724.8522082321100
9.47-13.432.6617891881100
13.4-47.7329.95916119196

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.16 Å47.73 Å
Translation3.16 Å47.73 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.5.1phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
EDNAdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3V8O

3v8o


Resolution: 3.16→47.73 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.921 / WRfactor Rfree: 0.2509 / WRfactor Rwork: 0.2052 / Occupancy max: 1 / Occupancy min: 0.01 / FOM work R set: 0.7868 / SU B: 52.014 / SU ML: 0.377 / SU R Cruickshank DPI: 0.9823 / SU Rfree: 0.4173 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.982 / ESU R Free: 0.417 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2768 345 5 %RANDOM
Rwork0.2265 ---
obs0.2288 6900 99.93 %-
all-6902 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 207.1 Å2 / Biso mean: 108.4827 Å2 / Biso min: 50.28 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0 Å2-0 Å2
2---0.01 Å2-0 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 3.16→47.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1439 0 0 2 1441
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0191479
X-RAY DIFFRACTIONr_angle_refined_deg1.8061.9722011
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.5715187
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.47124.33360
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.59615227
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.813157
X-RAY DIFFRACTIONr_chiral_restr0.1080.2217
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0221137
X-RAY DIFFRACTIONr_mcbond_it3.185.765756
X-RAY DIFFRACTIONr_mcangle_it5.0778.648940
X-RAY DIFFRACTIONr_scbond_it3.485.887720
LS refinement shellResolution: 3.16→3.242 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.456 24 -
Rwork0.359 456 -
all-480 -
obs-456 100 %
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)
110.96-1.1539-0.80623.4128-0.72745.1404-0.02730.60321.06560.0795-0.1441-1.1265-0.63820.22260.17140.32340.094-0.06460.27060.21950.593729.282444.50822.302
213.068-0.3058-0.82716.008-0.7073.65810.12732.30140.182-0.8739-0.6313-0.23970.24990.05530.5040.24160.18080.06380.75580.21570.157612.828141.4375-9.2908
37.3321-3.0577-11.44453.913714.7763.35090.5596-0.05021.44850.0847-0.1212-0.6869-1.3613-0.8138-0.43840.48170.1222-0.32920.21280.02540.967337.512942.19359.3237
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A572 - 663
2X-RAY DIFFRACTION2A664 - 756
3X-RAY DIFFRACTION3B577 - 585

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