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- PDB-1pz9: Modulation of agrin function by alternative splicing and Ca2+ binding -

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Basic information

Entry
Database: PDB / ID: 1pz9
TitleModulation of agrin function by alternative splicing and Ca2+ binding
ComponentsAgrin
KeywordsSTRUCTURAL PROTEIN / Agrin
Function / homology
Function and homology information


extracellular matrix of synaptic cleft / acetylcholine receptor regulator activity / positive regulation of synaptic assembly at neuromuscular junction / skeletal muscle acetylcholine-gated channel clustering / chondroitin sulfate binding / laminin-1 binding / sialic acid binding / neuron cell-cell adhesion / dystroglycan binding / basal part of cell ...extracellular matrix of synaptic cleft / acetylcholine receptor regulator activity / positive regulation of synaptic assembly at neuromuscular junction / skeletal muscle acetylcholine-gated channel clustering / chondroitin sulfate binding / laminin-1 binding / sialic acid binding / neuron cell-cell adhesion / dystroglycan binding / basal part of cell / photoreceptor ribbon synapse / filopodium assembly / glycosaminoglycan binding / heparan sulfate proteoglycan binding / extracellular matrix binding / positive regulation of filopodium assembly / neuromuscular junction development / transmembrane receptor protein tyrosine kinase activator activity / receptor clustering / basement membrane / laminin binding / extracellular matrix / positive regulation of GTPase activity / brain development / neuromuscular junction / negative regulation of neuron projection development / signaling receptor activity / nervous system development / heparin binding / actin cytoskeleton organization / cell differentiation / membrane raft / axon / glutamatergic synapse / synapse / calcium ion binding / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region / plasma membrane
Similarity search - Function
NtA (N-terminal agrin) domain / Agrin NtA domain / NtA (N-terminal agrin) domain profile. / Follistatin-like, N-terminal / Follistatin-N-terminal domain-like / Factor I / membrane attack complex / factor I membrane attack complex / : / Domain found in sea urchin sperm protein, enterokinase, agrin / Laminin G domain ...NtA (N-terminal agrin) domain / Agrin NtA domain / NtA (N-terminal agrin) domain profile. / Follistatin-like, N-terminal / Follistatin-N-terminal domain-like / Factor I / membrane attack complex / factor I membrane attack complex / : / Domain found in sea urchin sperm protein, enterokinase, agrin / Laminin G domain / Laminin-type EGF-like (LE) domain profile. / Laminin-type EGF-like (LE) domain signature. / Laminin-type epidermal growth factor-like domai / Laminin EGF domain / SEA domain superfamily / Kazal-type serine protease inhibitor domain / Laminin-type EGF domain / Kazal-type serine protease inhibitor domain / SEA domain profile. / SEA domain / SEA domain / Laminin G domain profile. / Kazal type serine protease inhibitors / Laminin G domain / Laminin G domain / Kazal domain superfamily / Kazal domain / Kazal domain profile. / Tissue inhibitor of metalloproteinases-like, OB-fold / EGF-like domain / EGF-type aspartate/asparagine hydroxylation site / Aspartic acid and asparagine hydroxylation site. / EGF-like calcium-binding domain / Calcium-binding EGF-like domain / Epidermal growth factor-like domain. / Jelly Rolls - #200 / EGF-like domain profile. / EGF-like domain signature 2. / EGF-like domain signature 1. / EGF-like domain / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsStetefeld, J. / Alexandrescu, A.T. / Maciejewski, M.W. / Jenny, M. / Rathgeb-Szabo, K. / Schulthess, T. / Landwehr, R. / Frank, S. / Ruegg, M.A. / Kammerer, R.A.
CitationJournal: STRUCTURE / Year: 2004
Title: Modulation of agrin function by alternative splicing and Ca2+ binding.
Authors: Stetefeld, J. / Alexandrescu, A.T. / Maciejewski, M.W. / Jenny, M. / Rathgeb-Szabo, K. / Schulthess, T. / Landwehr, R. / Frank, S. / Ruegg, M.A. / Kammerer, R.A.
History
DepositionJul 10, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 13, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Remark 999SEQUENCE the c-terminal agrin domain has alternative splice variants, we solved the structure of ...SEQUENCE the c-terminal agrin domain has alternative splice variants, we solved the structure of B11 (1pz7) and B8 with (1pz8) and without (1pz9) calcium, therefore the sequence-file conatins either 11 or 8 residues more than the so called B0-insert, the insert starts at TKS- and ends at EKA, B11:PDALDYPAEPS B8:HLSNEIPA however, not all the splice-residues are detectable in the electron density map

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Agrin
B: Agrin


Theoretical massNumber of molelcules
Total (without water)44,1042
Polymers44,1042
Non-polymers00
Water1,35175
1
A: Agrin


Theoretical massNumber of molelcules
Total (without water)22,0521
Polymers22,0521
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Agrin


Theoretical massNumber of molelcules
Total (without water)22,0521
Polymers22,0521
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)102.169, 56.751, 74.889
Angle α, β, γ (deg.)90.00, 127.04, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Agrin


Mass: 22052.047 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Fragment: Basal Lamina Domain / Gene: AGRN / Production host: Escherichia coli (E. coli) / References: UniProt: P31696
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.96 Å3/Da / Density % sol: 37.37 %
Crystal growTemperature: 276 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 276K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, Hamburg / Beamline: BW7B / Wavelength: 1 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.78→30.9 Å / Num. obs: 8472 / % possible obs: 99.2 % / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Rsym value: 0.102 / Net I/σ(I): 13.5

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Processing

Software
NameVersionClassification
REFMAC5refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→20 Å / Cor.coef. Fo:Fc: 0.897 / Cor.coef. Fo:Fc free: 0.898 / SU B: 29.275 / SU ML: 0.593 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.467 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27105 394 4.7 %RANDOM
Rwork0.2384 ---
obs0.2399 8056 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 22.696 Å2
Baniso -1Baniso -2Baniso -3
1--0.41 Å20 Å2-3.6 Å2
2--0.95 Å20 Å2
3----4.88 Å2
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2873 0 0 75 2948
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0212932
X-RAY DIFFRACTIONr_bond_other_d0.0010.022652
X-RAY DIFFRACTIONr_angle_refined_deg1.6051.9463975
X-RAY DIFFRACTIONr_angle_other_deg0.80836167
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.3833368
X-RAY DIFFRACTIONr_dihedral_angle_2_deg16.99415512
X-RAY DIFFRACTIONr_chiral_restr0.0840.2453
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023264
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02570
X-RAY DIFFRACTIONr_nbd_refined0.2770.3687
X-RAY DIFFRACTIONr_nbd_other0.2610.32803
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1580.5203
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1650.57
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2580.358
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3080.3134
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3180.514
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.7561.51839
X-RAY DIFFRACTIONr_mcangle_it1.38622948
X-RAY DIFFRACTIONr_scbond_it1.631093
X-RAY DIFFRACTIONr_scangle_it2.7244.51027
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.871 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.361 37
Rwork0.335 574
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)
11.0754-0.1796-0.22990.4367-1.21782.16340.0201-0.0920.0614-0.17650.04460.0360.21150.0107-0.06460.0251-0.06150.11380.3917-0.04030.750518.4428.0652.166
21.4322-0.645-0.6150.36370.66051.8810.02380.13260.03620.0341-0.0598-0.03050.2263-0.13560.0360.0362-0.03980.14570.3332-0.0250.7052.77817.51337.485
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA12 - 3012 - 30
2X-RAY DIFFRACTION1AA - C45 - 20445 - 3
3X-RAY DIFFRACTION2BB12 - 3012 - 30
4X-RAY DIFFRACTION2BB - D45 - 20445 - 3

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