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- PDB-2cm6: crystal structure of the C2B domain of rabphilin3A -

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Basic information

Entry
Database: PDB / ID: 2cm6
Titlecrystal structure of the C2B domain of rabphilin3A
ComponentsRABPHILIN-3A
KeywordsPROTEIN TRANSPORT / ZINC-FINGER / RABPHILIN3A / CA2+ BINDING / METAL-BINDING / SYNAPTIC EXOCYTOSIS / C2A-C2B LINKER FRAGMENT / C2B / ZINC / SYNAPSE / C2 DOMAIN / TRANSPORT
Function / homology
Function and homology information


selenium binding / spontaneous neurotransmitter secretion / regulation of calcium ion-dependent exocytosis / extrinsic component of synaptic vesicle membrane / cholinergic synapse / inositol 1,4,5 trisphosphate binding / calcium-dependent phospholipid binding / dendritic spine organization / regulation of NMDA receptor activity / extrinsic component of membrane ...selenium binding / spontaneous neurotransmitter secretion / regulation of calcium ion-dependent exocytosis / extrinsic component of synaptic vesicle membrane / cholinergic synapse / inositol 1,4,5 trisphosphate binding / calcium-dependent phospholipid binding / dendritic spine organization / regulation of NMDA receptor activity / extrinsic component of membrane / synaptic vesicle priming / phosphate ion binding / exocytosis / phosphatidylinositol-4,5-bisphosphate binding / secretory granule / intracellular protein transport / neuromuscular junction / phospholipid binding / small GTPase binding / synaptic vesicle membrane / synaptic vesicle / postsynaptic membrane / dendritic spine / neuron projection / calcium ion binding / synapse / protein-containing complex binding / protein-containing complex / zinc ion binding
Similarity search - Function
Rabphilin-3A / Rabphilin/DOC2/Noc2 / : / FYVE-type zinc finger / FYVE-type zinc finger / Rab-binding domain / Rab-binding domain profile. / Zinc finger, FYVE-related / Zinc finger FYVE/FYVE-related type profile. / Synaptotagmin ...Rabphilin-3A / Rabphilin/DOC2/Noc2 / : / FYVE-type zinc finger / FYVE-type zinc finger / Rab-binding domain / Rab-binding domain profile. / Zinc finger, FYVE-related / Zinc finger FYVE/FYVE-related type profile. / Synaptotagmin / C2 domain / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain / C2 domain profile. / C2 domain superfamily / Zinc finger, FYVE/PHD-type / Zinc finger, RING/FYVE/PHD-type / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
PHOSPHATE ION / Rabphilin-3A
Similarity search - Component
Biological speciesRATTUS NORVEGICUS (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsSchlicker, C. / Montaville, P. / Sheldrick, G.M. / Becker, S.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: The C2A-C2B Linker Defines the High Affinity Ca2+ Binding Mode of Rabphilin-3A.
Authors: Montaville, P. / Schlicker, C. / Leonov, A. / Zweckstetter, M. / Sheldrick, G.M. / Becker, S.
History
DepositionMay 4, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 4, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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.pdbx_dist_value / _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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RABPHILIN-3A
B: RABPHILIN-3A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4717
Polymers38,2162
Non-polymers2555
Water1,36976
1
A: RABPHILIN-3A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,1883
Polymers19,1081
Non-polymers802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: RABPHILIN-3A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2834
Polymers19,1081
Non-polymers1753
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)40.069, 59.606, 66.385
Angle α, β, γ (deg.)90.00, 103.89, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein RABPHILIN-3A / EXOPHILIN-1


Mass: 19107.816 Da / Num. of mol.: 2 / Fragment: C2B DOMAIN AND LINKER, RESIDUES 519-684
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Plasmid: PGEX-2T-RABPHILIN3A-519-684 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P47709
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


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


Mass: 18.015 Da / Num. of mol.: 76 / 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: 2.4 Å3/Da / Density % sol: 48 %
Description: FRAGMENT CONTAINING RESIDUES 540-677 OF 2CM5 WAS USED AS SEARCH MODEL
Crystal growDetails: 0.1 M HEPES PH 7.6, 25 % PEG 8000, 200 MM CA

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Data collection

DiffractionMean temperature: 89.7 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9536
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 21, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9536 Å / Relative weight: 1
ReflectionResolution: 1.85→43.76 Å / Num. obs: 25345 / % possible obs: 97.2 % / Observed criterion σ(I): 2.39 / Redundancy: 6.44 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 12.5
Reflection shellResolution: 1.85→1.94 Å / Redundancy: 4.43 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 3.07 / % possible all: 93.9

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Processing

Software
NameClassification
SHELXL-97refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2CM5

2cm5


Resolution: 1.85→43.76 Å / Num. restraintsaints: 9466 / Cross valid method: THROUGHOUT / σ(F): 2.39
RfactorNum. reflection% reflectionSelection details
Rfree0.2675 1270 5 %RANDOM
all0.1979 25345 --
obs0.1948 -97.2 %-
Refinement stepCycle: LAST / Resolution: 1.85→43.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2312 0 9 76 2397
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.005
X-RAY DIFFRACTIONs_angle_d0.021
X-RAY DIFFRACTIONs_similar_dist0.005
X-RAY DIFFRACTIONs_from_restr_planes0.0266
X-RAY DIFFRACTIONs_zero_chiral_vol0.029
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.038
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.275
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.08
X-RAY DIFFRACTIONs_approx_iso_adps0

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