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- PDB-4z89: SH3-II of Drosophila Rim-binding protein bound to a Cacophony der... -

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Basic information

Entry
Database: PDB / ID: 4z89
TitleSH3-II of Drosophila Rim-binding protein bound to a Cacophony derived peptide
Components
  • RIM-binding protein, isoform F
  • Voltage-dependent calcium channel type A subunit alpha-1
KeywordsRIM-BINDING PROTEIN / Synapse / Active Zone / SH3 domain / Cacophony peptide
Function / homology
Function and homology information


regulation of membrane potential in photoreceptor cell / Presynaptic depolarization and calcium channel opening / Regulation of insulin secretion / presynaptic active zone organization / Pregnenolone biosynthesis / Serotonin Neurotransmitter Release Cycle / Norepinephrine Neurotransmitter Release Cycle / Glutamate Neurotransmitter Release Cycle / Dopamine Neurotransmitter Release Cycle / Acetylcholine Neurotransmitter Release Cycle ...regulation of membrane potential in photoreceptor cell / Presynaptic depolarization and calcium channel opening / Regulation of insulin secretion / presynaptic active zone organization / Pregnenolone biosynthesis / Serotonin Neurotransmitter Release Cycle / Norepinephrine Neurotransmitter Release Cycle / Glutamate Neurotransmitter Release Cycle / Dopamine Neurotransmitter Release Cycle / Acetylcholine Neurotransmitter Release Cycle / cytoskeleton of presynaptic active zone / cytoskeletal matrix organization at active zone / low voltage-gated calcium channel activity / male courtship behavior, veined wing generated song production / positive regulation of synaptic assembly at neuromuscular junction / courtship behavior / visual behavior / epithelial fluid transport / high voltage-gated calcium channel activity / presynaptic active zone cytoplasmic component / detection of light stimulus involved in visual perception / regulation of neurotransmitter secretion / neuromuscular synaptic transmission / neurotransmitter secretion / presynaptic active zone / voltage-gated calcium channel complex / neuron remodeling / exocytosis / calcium ion import across plasma membrane / positive regulation of calcium ion transport into cytosol / autophagosome maturation / phototransduction / voltage-gated calcium channel activity / regulation of heart rate / adult locomotory behavior / neuromuscular junction / calcium-mediated signaling / neuron cellular homeostasis / calcium ion transmembrane transport / autophagy / calcium ion transport / basolateral plasma membrane / chemical synaptic transmission / apical plasma membrane / calcium ion binding / metal ion binding
Similarity search - Function
RIMS-binding protein, second SH3 domain / RIMS-binding protein, third SH3 domain / RIMS-binding protein 1/2/3 / Voltage-dependent calcium channel, alpha-1 subunit, IQ domain / Voltage gated calcium channel IQ domain / Voltage gated calcium channel IQ domain / Voltage-dependent calcium channel, alpha-1 subunit / Voltage-dependent L-type calcium channel, IQ-associated domain / Voltage-dependent L-type calcium channel, IQ-associated / : ...RIMS-binding protein, second SH3 domain / RIMS-binding protein, third SH3 domain / RIMS-binding protein 1/2/3 / Voltage-dependent calcium channel, alpha-1 subunit, IQ domain / Voltage gated calcium channel IQ domain / Voltage gated calcium channel IQ domain / Voltage-dependent calcium channel, alpha-1 subunit / Voltage-dependent L-type calcium channel, IQ-associated domain / Voltage-dependent L-type calcium channel, IQ-associated / : / Variant SH3 domain / Variant SH3 domain / SH3 Domains / Voltage-dependent channel domain superfamily / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / SH3 type barrels. / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / EF-hand calcium-binding domain profile. / EF-hand domain / Ion transport domain / Ion transport protein / Roll / Immunoglobulin-like fold / Mainly Beta
Similarity search - Domain/homology
RIM-binding protein, isoform F / Voltage-dependent calcium channel type A subunit alpha-1
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.64 Å
AuthorsDriller, J.H. / Holton, N. / Siebert, M. / Boehme, M.A. / Wahl, M.C. / Sigrist, S.J. / Loll, B.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationSFB958 Germany
CitationJournal: Elife / Year: 2015
Title: A high affinity RIM-binding protein/Aplip1 interaction prevents the formation of ectopic axonal active zones.
Authors: Siebert, M. / Bohme, M.A. / Driller, J.H. / Babikir, H. / Mampell, M.M. / Rey, U. / Ramesh, N. / Matkovic, T. / Holton, N. / Reddy-Alla, S. / Gottfert, F. / Kamin, D. / Quentin, C. / ...Authors: Siebert, M. / Bohme, M.A. / Driller, J.H. / Babikir, H. / Mampell, M.M. / Rey, U. / Ramesh, N. / Matkovic, T. / Holton, N. / Reddy-Alla, S. / Gottfert, F. / Kamin, D. / Quentin, C. / Klinedinst, S. / Andlauer, T.F. / Hell, S.W. / Collins, C.A. / Wahl, M.C. / Loll, B. / Sigrist, S.J.
History
DepositionApr 8, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 5, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_audit_support / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RIM-binding protein, isoform F
B: RIM-binding protein, isoform F
C: RIM-binding protein, isoform F
D: RIM-binding protein, isoform F
E: RIM-binding protein, isoform F
F: RIM-binding protein, isoform F
G: RIM-binding protein, isoform F
H: RIM-binding protein, isoform F
I: RIM-binding protein, isoform F
J: RIM-binding protein, isoform F
a: Voltage-dependent calcium channel type A subunit alpha-1
b: Voltage-dependent calcium channel type A subunit alpha-1
c: Voltage-dependent calcium channel type A subunit alpha-1
d: Voltage-dependent calcium channel type A subunit alpha-1
e: Voltage-dependent calcium channel type A subunit alpha-1
f: Voltage-dependent calcium channel type A subunit alpha-1
g: Voltage-dependent calcium channel type A subunit alpha-1
h: Voltage-dependent calcium channel type A subunit alpha-1
i: Voltage-dependent calcium channel type A subunit alpha-1
j: Voltage-dependent calcium channel type A subunit alpha-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,28021
Polymers99,24020
Non-polymers401
Water2,414134
1
A: RIM-binding protein, isoform F
a: Voltage-dependent calcium channel type A subunit alpha-1


Theoretical massNumber of molelcules
Total (without water)9,9242
Polymers9,9242
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: RIM-binding protein, isoform F
b: Voltage-dependent calcium channel type A subunit alpha-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,9643
Polymers9,9242
Non-polymers401
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: RIM-binding protein, isoform F
c: Voltage-dependent calcium channel type A subunit alpha-1


Theoretical massNumber of molelcules
Total (without water)9,9242
Polymers9,9242
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: RIM-binding protein, isoform F
d: Voltage-dependent calcium channel type A subunit alpha-1


Theoretical massNumber of molelcules
Total (without water)9,9242
Polymers9,9242
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: RIM-binding protein, isoform F
e: Voltage-dependent calcium channel type A subunit alpha-1


Theoretical massNumber of molelcules
Total (without water)9,9242
Polymers9,9242
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: RIM-binding protein, isoform F
f: Voltage-dependent calcium channel type A subunit alpha-1


Theoretical massNumber of molelcules
Total (without water)9,9242
Polymers9,9242
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: RIM-binding protein, isoform F
g: Voltage-dependent calcium channel type A subunit alpha-1


Theoretical massNumber of molelcules
Total (without water)9,9242
Polymers9,9242
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: RIM-binding protein, isoform F
h: Voltage-dependent calcium channel type A subunit alpha-1


Theoretical massNumber of molelcules
Total (without water)9,9242
Polymers9,9242
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
I: RIM-binding protein, isoform F
i: Voltage-dependent calcium channel type A subunit alpha-1


Theoretical massNumber of molelcules
Total (without water)9,9242
Polymers9,9242
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
10
J: RIM-binding protein, isoform F
j: Voltage-dependent calcium channel type A subunit alpha-1


Theoretical massNumber of molelcules
Total (without water)9,9242
Polymers9,9242
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.300, 122.220, 68.540
Angle α, β, γ (deg.)90.00, 113.17, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
RIM-binding protein, isoform F


Mass: 8277.036 Da / Num. of mol.: 10 / Fragment: UNP residues 1318-1382
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Rbp, Dmel_CG43073 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0B4JDC9
#2: Protein/peptide
Voltage-dependent calcium channel type A subunit alpha-1 / Protein cacophony / Protein nightblind A / Protein no-on-transient B / Dmca1A


Mass: 1646.976 Da / Num. of mol.: 10 / Fragment: UNP residues 1688-1702 / Source method: obtained synthetically / Source: (synth.) Drosophila melanogaster (fruit fly) / References: UniProt: P91645
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45.63 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 100 mM MES pH 6.0, 200 mM Calciumacetate, 20% PEG 8000
PH range: 6.0-6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Nov 19, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2.64→50 Å / Num. obs: 25229 / % possible obs: 96.9 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.166 / Net I/σ(I): 8
Reflection shellResolution: 2.64→2.74 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.71 / Mean I/σ(I) obs: 2.1 / % possible all: 95

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4Z88

4z88


Resolution: 2.64→43.868 Å / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 35.55 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.312 1322 5.24 %
Rwork0.2554 --
obs0.2582 25229 97.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.64→43.868 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6088 0 1 134 6223
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0056305
X-RAY DIFFRACTIONf_angle_d1.1368530
X-RAY DIFFRACTIONf_dihedral_angle_d13.0732379
X-RAY DIFFRACTIONf_chiral_restr0.049799
X-RAY DIFFRACTIONf_plane_restr0.0071171
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6401-2.74580.48691370.36742597X-RAY DIFFRACTION90
2.7458-2.87070.36641380.35782625X-RAY DIFFRACTION92
2.8707-3.0220.34851400.29422661X-RAY DIFFRACTION93
3.022-3.21120.30911420.25662695X-RAY DIFFRACTION93
3.2112-3.45890.32261400.25122658X-RAY DIFFRACTION93
3.4589-3.80660.30981400.24922651X-RAY DIFFRACTION91
3.8066-4.35650.28491370.22492618X-RAY DIFFRACTION91
4.3565-5.48520.25971430.21442703X-RAY DIFFRACTION94
5.4852-34.65110.28761450.24992751X-RAY DIFFRACTION94
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)
12.17260.0867-1.33271.7175-0.4031.75810.35870.31720.07280.259-0.03090.264-0.0075-0.2937-0.11170.37360.0314-0.16660.2874-0.08120.3894-24.963723.0767-7.7974
23.1081-0.1659-0.63693.8251-0.36252.6131-0.10980.10720.1196-0.12050.1265-0.3243-0.1760.027-0.06680.32140.08-0.10480.18-0.08820.3775-3.161123.1925-13.1541
32.839-0.2236-1.01862.36720.08653.96040.095-0.30110.3774-0.13080.14920.00270.1215-0.2775-0.20140.23060.0691-0.07860.3638-0.1190.3618-12.46267.75039.5961
42.84460.6685-1.58823.2145-0.74833.57360.1994-0.4305-0.2173-0.19-0.3146-0.0037-0.46530.33850.08190.38520.1137-0.10120.4337-0.08280.2564-15.78977.7353-30.5413
52.79860.6858-0.78631.5449-1.11620.8903-0.77010.0418-0.1662-0.42190.0041-0.1246-0.4133-0.2651-0.27710.45260.0276-0.23260.5031-0.20830.2655-38.056911.094-27.6793
64.4132-0.25231.27362.5714-0.98615.4632-0.34940.14140.15260.42730.0153-0.1385-0.86080.23460.25570.31160.0675-0.14360.3722-0.04620.325310.086611.15586.7888
71.3637-0.72550.02650.8636-0.02480.86630.17280.63560.17290.00610.0880.02090.0363-0.47480.20720.1729-0.064-0.29190.44660.11730.5618-21.451648.5764-2.3077
83.0552-0.0847-0.42882.5489-2.02581.70230.05930.0614-0.4868-0.340.06270.10120.1743-1.1756-0.10370.7089-0.1474-0.07450.8683-0.06110.3919.6352-12.6062-23.3081
95.23272.3567-1.03623.5185-2.35954.4155-0.35460.53070.0141-0.13580.13-0.55120.71070.33480.21620.35670.0898-0.03340.3706-0.12520.5764-26.3733-14.5764-21.5525
101.17960.7717-0.422.01390.12813.466-0.2870.14290.5274-0.13830.19570.22780.1448-0.5406-0.04410.41570.0173-0.17120.22210.02730.513-1.235-14.91160.628
113.03021.1098-0.23130.7332-1.16183.5722-0.1695-0.4147-0.10790.3842-0.00010.35120.1286-0.01180.21690.29880.07910.04740.22340.02260.8143-22.595322.03143.0404
124.36692.858-1.79513.46841.01843.75610.11940.8169-0.0031-0.46160.29260.301-0.5459-0.51240.07110.6550.1456-0.24710.433-0.08420.3153-5.43519.6198-23.4174
131.15891.2891.29141.48221.68372.80050.0888-0.3444-0.19140.5385-0.0713-0.04780.51290.2965-0.19410.72130.2245-0.11950.5666-0.24030.2378-9.9529-2.682111.8465
145.2214-2.08740.42256.2915-0.77582.2548-0.0110.1901-0.44930.06460.05670.55720.08330.1428-0.15470.32210.2635-0.0450.4258-0.03720.5239-17.9712-2.5486-33.0907
151.4810.37260.78170.93460.49751.40170.0691-0.1445-0.0358-0.191-0.16620.1185-0.2902-0.1893-0.04140.6316-0.127-0.12990.6075-0.21680.3077-37.696716.9805-18.6474
167.9242-1.2857-0.69114.764-1.0956.044-0.60370.29540.23840.1354-0.411-0.0395-0.75490.46060.81620.55910.0571-0.29410.62470.10910.32119.854816.0097-3.4314
174.2727-1.5783-3.18074.98221.02788.2232-0.12770.99440.72560.2636-0.154-0.0509-0.56210.23810.14350.3062-0.0507-0.00650.40910.24170.5191-21.27759.3965-5.1862
180.170.0316-0.06910.0109-0.08120.9307-0.02750.17240.1552-0.1122-0.09960.0228-0.5564-0.04760.14851.48420.0235-0.43930.87850.00980.43369.1562-1.8485-26.6719
196.2984-0.1340.18671.7157-1.54875.49910.1807-0.6263-0.5210.29180.5034-0.83040.50360.6296-0.58580.64160.0834-0.02160.3529-0.05990.6539-25.988-15.3939-10.5708
202.94760.8387-1.70281.9223-2.58963.60940.07710.8949-0.0677-0.11440.61310.19340.86670.1888-0.29590.6180.0895-0.30090.5132-0.09810.58010.2304-20.7065-8.1919
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A'
2X-RAY DIFFRACTION2chain 'B'
3X-RAY DIFFRACTION3chain 'C'
4X-RAY DIFFRACTION4chain 'D'
5X-RAY DIFFRACTION5chain 'E'
6X-RAY DIFFRACTION6chain 'F'
7X-RAY DIFFRACTION7chain 'G'
8X-RAY DIFFRACTION8chain 'H'
9X-RAY DIFFRACTION9chain 'I'
10X-RAY DIFFRACTION10chain 'J'
11X-RAY DIFFRACTION11chain 'a'
12X-RAY DIFFRACTION12chain 'b'
13X-RAY DIFFRACTION13chain 'c'
14X-RAY DIFFRACTION14chain 'd'
15X-RAY DIFFRACTION15chain 'e'
16X-RAY DIFFRACTION16chain 'f'
17X-RAY DIFFRACTION17chain 'g'
18X-RAY DIFFRACTION18chain 'h'
19X-RAY DIFFRACTION19chain 'i'
20X-RAY DIFFRACTION20chain 'j'

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