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- PDB-6q9m: Central Fibronectin-III array of RIM-binding protein -

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Basic information

Entry
Database: PDB / ID: 6q9m
TitleCentral Fibronectin-III array of RIM-binding protein
ComponentsRIM-binding protein, isoform F
KeywordsEXOCYTOSIS / Active Zone / RIM-binding protein / Fibronectin type III / FN-III
Function / homology
Function and homology information


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 / cytoskeletal matrix organization at active zone / cytoskeleton of presynaptic active zone / neuromuscular synaptic transmission ...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 / cytoskeletal matrix organization at active zone / cytoskeleton of presynaptic active zone / neuromuscular synaptic transmission / presynaptic active zone cytoplasmic component / neuromuscular junction / metal ion binding
Similarity search - Function
RIMS-binding protein, second SH3 domain / RIMS-binding protein, third SH3 domain / RIMS-binding protein 1/2/3 / Variant SH3 domain / Variant SH3 domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Src homology 3 domains ...RIMS-binding protein, second SH3 domain / RIMS-binding protein, third SH3 domain / RIMS-binding protein 1/2/3 / Variant SH3 domain / Variant SH3 domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Immunoglobulin-like fold
Similarity search - Domain/homology
PHOSPHATE ION / RIM-binding protein, isoform F
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.453 Å
AuthorsDriller, J.D. / Habibi, S. / Wahl, M.C. / Loll, B.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationSFB958 Germany
CitationJournal: J.Cell Biol. / Year: 2020
Title: RIM-binding protein couples synaptic vesicle recruitment to release sites.
Authors: Petzoldt, A.G. / Gotz, T.W.B. / Driller, J.H. / Lutzkendorf, J. / Reddy-Alla, S. / Matkovic-Rachid, T. / Liu, S. / Knoche, E. / Mertel, S. / Ugorets, V. / Lehmann, M. / Ramesh, N. / ...Authors: Petzoldt, A.G. / Gotz, T.W.B. / Driller, J.H. / Lutzkendorf, J. / Reddy-Alla, S. / Matkovic-Rachid, T. / Liu, S. / Knoche, E. / Mertel, S. / Ugorets, V. / Lehmann, M. / Ramesh, N. / Beuschel, C.B. / Kuropka, B. / Freund, C. / Stelzl, U. / Loll, B. / Liu, F. / Wahl, M.C. / Sigrist, S.J.
History
DepositionDec 18, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 15, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 15, 2020Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.year
Revision 1.2May 13, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3May 15, 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: RIM-binding protein, isoform F
B: RIM-binding protein, isoform F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,1123
Polymers65,0172
Non-polymers951
Water70339
1
A: RIM-binding protein, isoform F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6042
Polymers32,5091
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: RIM-binding protein, isoform F


Theoretical massNumber of molelcules
Total (without water)32,5091
Polymers32,5091
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.095, 80.547, 93.077
Angle α, β, γ (deg.)90.00, 99.03, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein RIM-binding protein, isoform F


Mass: 32508.629 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly)
Gene: Rbp, CG14867, CG31302, CG5143, CG5152, Dmel\CG43073, DRBP, drbp, RBP, rbp, CG43073, Dmel_CG43073
Plasmid: pGex-6p1 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A0B4JDC9
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / 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: 2.91 Å3/Da / Density % sol: 57.72 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.4M KH2PO4, 18% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: May 14, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2.45→50 Å / Num. obs: 27284 / % possible obs: 99.4 % / Redundancy: 3.3 % / CC1/2: 0.998 / Rrim(I) all: 0.05 / Net I/σ(I): 18.2
Reflection shellResolution: 2.45→2.6 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 2.14 / Num. unique obs: 4373 / CC1/2: 0.798 / Rrim(I) all: 0.71 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XSCALEdata scaling
SHARPphasing
BUCCANEERmodel building
RefinementMethod to determine structure: MAD / Resolution: 2.453→41.569 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 28.66
RfactorNum. reflection% reflection
Rfree0.2596 1365 5 %
Rwork0.2108 --
obs0.2133 27276 99.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.453→41.569 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4002 0 5 39 4046
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084097
X-RAY DIFFRACTIONf_angle_d1.0895593
X-RAY DIFFRACTIONf_dihedral_angle_d11.4582980
X-RAY DIFFRACTIONf_chiral_restr0.06663
X-RAY DIFFRACTIONf_plane_restr0.01722
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4529-2.54050.31951340.30162537X-RAY DIFFRACTION99
2.5405-2.64220.32251360.27482585X-RAY DIFFRACTION100
2.6422-2.76250.34731360.26732580X-RAY DIFFRACTION100
2.7625-2.90810.28311370.25722607X-RAY DIFFRACTION100
2.9081-3.09020.32961370.25232607X-RAY DIFFRACTION100
3.0902-3.32870.2681360.22932579X-RAY DIFFRACTION100
3.3287-3.66350.30511370.22212603X-RAY DIFFRACTION99
3.6635-4.19320.24991360.20672574X-RAY DIFFRACTION99
4.1932-5.28130.21751370.16772618X-RAY DIFFRACTION99
5.2813-41.57540.2291390.19682621X-RAY DIFFRACTION98
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)
18.9966-1.62981.92215.5379-0.66956.52770.18730.40740.241-0.0141-0.2797-0.2904-0.12690.58720.10920.3030.08980.02610.52010.01720.45614.70943.69736.7036
27.18650.23013.66793.0194-1.07916.02070.07980.0736-0.23430.0168-0.154-0.16010.40650.1390.09090.3075-0.04830.08210.3218-0.050.4331-16.68191.720928.8775
32.70051.53020.15118.79516.3425.04970.3443-0.6221-0.0854-0.5551-0.42990.37420.2875-1.35410.02210.8245-0.1177-0.17471.0184-0.16320.6715-32.089629.296933.9526
48.4342-0.4841-0.05443.9421-0.8256.4030.1920.4056-0.291-0.6795-0.21670.1160.47140.03130.02830.78740.1827-0.07550.55650.00480.429.4054-6.1742-10.9686
55.0605-0.7832.04534.2202-1.32827.02320.23840.17620.0377-0.4892-0.2176-0.0790.1759-0.1915-0.02650.38130.0006-0.01970.3514-0.07530.490716.464-3.112611.801
67.8545.00620.26078.6268-1.49073.61250.0946-0.5942-0.23850.4631-0.2172-0.1010.3722-0.33630.14060.6501-0.12990.00020.54740.03260.47994.9565-30.178429.4769
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 741 through 835 )
2X-RAY DIFFRACTION2chain 'A' and (resid 836 through 941 )
3X-RAY DIFFRACTION3chain 'A' and (resid 942 through 1036 )
4X-RAY DIFFRACTION4chain 'B' and (resid 742 through 835 )
5X-RAY DIFFRACTION5chain 'B' and (resid 836 through 941 )
6X-RAY DIFFRACTION6chain 'B' and (resid 942 through 1042 )

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