[English] 日本語
Yorodumi
- PDB-2x3v: Structure of The F-BAR Domain of Mouse Syndapin I -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2x3v
TitleStructure of The F-BAR Domain of Mouse Syndapin I
ComponentsPROTEIN KINASE C AND CASEIN KINASE SUBSTRATE IN NEURONS PROTEIN 1
KeywordsENDOCYTOSIS / BAR / N-WASP / DYNAMIN / PACSIN 1
Function / homology
Function and homology information


presynaptic endocytic zone / plasma membrane tubulation / COPI-coated vesicle / photoreceptor ribbon synapse / Clathrin-mediated endocytosis / negative regulation of endocytosis / protein localization to membrane / regulation of postsynaptic neurotransmitter receptor internalization / positive regulation of dendrite development / regulation of endocytosis ...presynaptic endocytic zone / plasma membrane tubulation / COPI-coated vesicle / photoreceptor ribbon synapse / Clathrin-mediated endocytosis / negative regulation of endocytosis / protein localization to membrane / regulation of postsynaptic neurotransmitter receptor internalization / positive regulation of dendrite development / regulation of endocytosis / synaptic vesicle endocytosis / axon terminus / cytoskeleton organization / cytoskeletal protein binding / neuron projection morphogenesis / actin filament organization / protein localization to plasma membrane / postsynaptic density membrane / phospholipid binding / cytoplasmic vesicle membrane / ruffle membrane / myelin sheath / endosome / synapse / glutamatergic synapse / perinuclear region of cytoplasm / signal transduction / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
PACSIN1, F-BAR / PACSIN1/PACSIN2, SH3 domain / Arfaptin homology (AH) domain/BAR domain / Fes/CIP4, and EFC/F-BAR homology domain / Fes/CIP4 homology domain / FCH domain / F-BAR domain / F-BAR domain profile. / AH/BAR domain superfamily / Variant SH3 domain ...PACSIN1, F-BAR / PACSIN1/PACSIN2, SH3 domain / Arfaptin homology (AH) domain/BAR domain / Fes/CIP4, and EFC/F-BAR homology domain / Fes/CIP4 homology domain / FCH domain / F-BAR domain / F-BAR domain profile. / AH/BAR domain superfamily / Variant SH3 domain / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Protein kinase C and casein kinase substrate in neurons protein 1
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.45 Å
AuthorsMa, Q. / Rao, Y. / Vahedi-Faridi, A. / Saenger, W. / Haucke, V.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Molecular Basis for SH3 Domain Regulation of F-Bar-Mediated Membrane Deformation.
Authors: Rao, Y. / Ma, Q. / Vahedi-Faridi, A. / Sundborger, A. / Pechstein, A. / Puchkov, D. / Luo, L. / Shupliakov, O. / Saenger, W. / Haucke, V.
History
DepositionJan 27, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 7, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PROTEIN KINASE C AND CASEIN KINASE SUBSTRATE IN NEURONS PROTEIN 1
B: PROTEIN KINASE C AND CASEIN KINASE SUBSTRATE IN NEURONS PROTEIN 1
C: PROTEIN KINASE C AND CASEIN KINASE SUBSTRATE IN NEURONS PROTEIN 1


Theoretical massNumber of molelcules
Total (without water)118,0483
Polymers118,0483
Non-polymers00
Water2,846158
1
A: PROTEIN KINASE C AND CASEIN KINASE SUBSTRATE IN NEURONS PROTEIN 1
B: PROTEIN KINASE C AND CASEIN KINASE SUBSTRATE IN NEURONS PROTEIN 1


Theoretical massNumber of molelcules
Total (without water)78,6992
Polymers78,6992
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9220 Å2
ΔGint-78.3 kcal/mol
Surface area32540 Å2
MethodPISA
2
C: PROTEIN KINASE C AND CASEIN KINASE SUBSTRATE IN NEURONS PROTEIN 1

C: PROTEIN KINASE C AND CASEIN KINASE SUBSTRATE IN NEURONS PROTEIN 1


Theoretical massNumber of molelcules
Total (without water)78,6992
Polymers78,6992
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area9120 Å2
ΔGint-76.1 kcal/mol
Surface area32590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.060, 153.490, 213.290
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein PROTEIN KINASE C AND CASEIN KINASE SUBSTRATE IN NEURONS PROTEIN 1 / SYNDAPIN I


Mass: 39349.430 Da / Num. of mol.: 3 / Fragment: F-BAR DOMAIN, RESIDUES 1-337
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q61644
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 158 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE PROTEIN CRYSTALLIZED IS ONLY THE N-TERMINAL F-BAR DOMAIN OF MOUSE SYNDAPIN I

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.1 Å3/Da / Density % sol: 60 % / Description: NONE
Crystal growpH: 5.5
Details: 2UL SYNDAPIN-I/EHD-1(401 -534)(25MG/ML IN 50MM HEPES,200MM NACL) MIXED WITH WELL SOLUTION 0.1M SODIUM CITRATE BUFFER (PH5.5),0.2M NAAC,10%(W/V) PEG4000. ONLY F-BAR DOMAIN OF SYDAPIN I CRYSTALLIZED.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.978
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 15, 2009
Details: DOUBLE CRYSTAL MONOCHROMATOR WITH 2 SETS OF MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.45→76.75 Å / Num. obs: 50261 / % possible obs: 97.2 % / Observed criterion σ(I): -3 / Redundancy: 6.69 % / Biso Wilson estimate: 55.7 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 16.35
Reflection shellResolution: 2.45→2.55 Å / Redundancy: 3.96 % / Rmerge(I) obs: 0.84 / Mean I/σ(I) obs: 1.84 / % possible all: 81.8

-
Processing

Software
NameVersionClassification
REFMAC5.3.0040refinement
XDSdata reduction
XDSdata scaling
XPREPphasing
SHELXDphasing
SHELXEphasing
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 2.45→76.7 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.934 / SU B: 15.91 / SU ML: 0.168 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.337 / ESU R Free: 0.255 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.26026 2448 4.9 %RANDOM
Rwork0.21152 ---
obs0.21402 47811 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.69 Å2
Baniso -1Baniso -2Baniso -3
1-0.71 Å20 Å20 Å2
2---5.65 Å20 Å2
3---4.94 Å2
Refinement stepCycle: LAST / Resolution: 2.45→76.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7261 0 0 158 7419
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0227405
X-RAY DIFFRACTIONr_bond_other_d0.0010.025325
X-RAY DIFFRACTIONr_angle_refined_deg0.9291.9469925
X-RAY DIFFRACTIONr_angle_other_deg0.774312947
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.535871
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.02325.038399
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.901151489
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.4281551
X-RAY DIFFRACTIONr_chiral_restr0.0550.21001
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.028146
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021450
X-RAY DIFFRACTIONr_nbd_refined0.1940.21872
X-RAY DIFFRACTIONr_nbd_other0.160.25072
X-RAY DIFFRACTIONr_nbtor_refined0.1730.23582
X-RAY DIFFRACTIONr_nbtor_other0.0870.23711
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1350.2211
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1250.231
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1670.2119
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2410.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.35425788
X-RAY DIFFRACTIONr_mcbond_other0.22621760
X-RAY DIFFRACTIONr_mcangle_it1.66736978
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.60543628
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.71952947
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.45→2.514 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rwork0.358 3025 -
Rfree-0 -
obs--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)
10.6093-2.0544-0.300514.27633.44270.95130.09590.07040.1364-0.7658-0.0173-0.4173-0.28240.1193-0.07860.26540.07020.07830.2005-0.01030.178971.982155.88735.3204
21.5605-3.09270.001916.82651.38220.42670.08030.179-0.2081-1.3758-0.01220.827-0.2864-0.1063-0.06820.34280.095-0.06440.2727-0.10540.079168.663232.454126.3965
31.31421.781-0.037610.5124.44212.49390.3043-0.05460.2648-0.94410.472-1.0394-0.11480.9111-0.77630.2834-0.01130.17720.382-0.10220.513672.618393.179946.1742
414.1697.52456.33417.97614.03782.9457-0.674-0.05910.12220.38560.4109-0.4423-0.64690.78740.2630.5186-0.41350.15150.5158-0.24270.386284.1531119.624863.9089
50.4802-0.5276-0.10047.90172.18410.62320.05170.1488-0.1975-0.4179-0.35231.42-0.1109-0.04670.30060.26430.0762-0.00050.2232-0.06040.220164.009136.79234.9906
60.4114-2.21-0.766815.12153.83061.4550.06530.134-0.1359-0.39220.0638-0.2137-0.05810.0424-0.12910.13420.081-0.01970.2588-0.14230.2280.76529.630329.0197
72.0307-3.4943-0.274312.57561.17511.1154-0.1929-0.05950.19440.86280.4559-0.529-0.05820.1118-0.26310.2590.07-0.00180.2232-0.08470.122677.441435.739442.5541
80.5158-0.8090.25274.34962.71833.2726-0.0090.4423-0.122-0.49620.1839-0.20370.11850.2866-0.17490.3748-0.01010.02930.4612-0.32860.384585.4157-31.95756.6595
90.3031-1.1853-0.79378.8813.89352.2251-0.19560.1435-0.38550.9003-0.02490.7020.4236-0.00750.22060.22610.0769-0.0340.2019-0.18030.422874.49-6.916732.5077
100.3646-1.5522-0.52628.27232.49830.7995-0.1049-0.04380.12371.51350.10990.02030.38890.2174-0.0050.45840.09810.03550.2170.01050.362365.873565.521351.8274
110.541-0.0969-0.23151.39350.99150.8429-0.04290.1124-0.1618-0.25260.07230.2639-0.13950.0658-0.02940.21160.0157-0.08210.3539-0.28640.47214.8415-19.0318-15.1596
126.80349.4938-3.178713.4593-3.58824.8871-0.3765-0.93730.1089-0.6624-0.0169-0.30020.4441-0.34940.39340.10360.00630.1380.5252-0.18371.35072.7779-87.5087-22.1914
130.6387-0.016-0.483318.27872.65830.7488-0.2760.0585-0.0237-1.30360.39020.546-0.15110.0077-0.11420.26060.0273-0.14390.452-0.38090.52122.7537-46.2234-27.3333
140.8451-0.26020.100312.01777.48084.7386-0.06750.0830.139-0.99890.7076-0.7107-0.55060.5916-0.64010.2507-0.11110.12050.3881-0.37790.504828.747610.24310.5575
157.45620.3115-1.84980.6759-0.37993.1335-0.01880.64230.7818-1.44440.0210.9197-0.5369-0.316-0.00220.5736-0.0046-0.16420.3843-0.29970.609117.151461.539216.6144
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A14 - 61
2X-RAY DIFFRACTION2A62 - 122
3X-RAY DIFFRACTION3A123 - 170
4X-RAY DIFFRACTION4A171 - 203
5X-RAY DIFFRACTION5A204 - 304
6X-RAY DIFFRACTION6B13 - 60
7X-RAY DIFFRACTION7B61 - 117
8X-RAY DIFFRACTION8B118 - 205
9X-RAY DIFFRACTION9B206 - 259
10X-RAY DIFFRACTION10B260 - 304
11X-RAY DIFFRACTION11C14 - 166
12X-RAY DIFFRACTION12C167 - 204
13X-RAY DIFFRACTION13C205 - 238
14X-RAY DIFFRACTION14C239 - 291
15X-RAY DIFFRACTION15C292 - 304

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more