[English] 日本語
Yorodumi
- PDB-2fic: The crystal structure of the BAR domain from human Bin1/Amphiphys... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2fic
TitleThe crystal structure of the BAR domain from human Bin1/Amphiphysin II and its implications for molecular recognition
ComponentsMyc box-dependent-interacting protein 1
KeywordsENDOCYTOSIS/EXOCYTOSIS / MEMBRANE PROTEIN / BAR domain / homodimer / coiled-coils / MEMBRANE PROTEIN COMPLEX / ENDOCYTOSIS-EXOCYTOSIS
Function / homology
Function and homology information


lipid tube / negative regulation of ventricular cardiac muscle cell action potential / negative regulation of calcium ion transmembrane transport via high voltage-gated calcium channel / negative regulation of aspartic-type endopeptidase activity involved in amyloid precursor protein catabolic process / lipid tube assembly / RNA polymerase II transcription repressor complex / regulation of cell cycle process / T-tubule organization / negative regulation of potassium ion transmembrane transport / varicosity ...lipid tube / negative regulation of ventricular cardiac muscle cell action potential / negative regulation of calcium ion transmembrane transport via high voltage-gated calcium channel / negative regulation of aspartic-type endopeptidase activity involved in amyloid precursor protein catabolic process / lipid tube assembly / RNA polymerase II transcription repressor complex / regulation of cell cycle process / T-tubule organization / negative regulation of potassium ion transmembrane transport / varicosity / extrinsic component of synaptic vesicle membrane / axon initial segment / cerebellar mossy fiber / positive regulation of astrocyte differentiation / nucleus localization / node of Ranvier / aspartic-type endopeptidase inhibitor activity / I band / RNA polymerase binding / nucleus organization / regulation of neuron differentiation / clathrin binding / endosome to lysosome transport / negative regulation of amyloid-beta formation / positive regulation of endocytosis / positive regulation of actin filament polymerization / regulation of heart rate by cardiac conduction / synaptic vesicle endocytosis / axon terminus / cytoskeleton organization / T-tubule / phospholipid binding / tau protein binding / Z disc / endocytosis / actin filament binding / synaptic vesicle / actin cytoskeleton / GTPase binding / Clathrin-mediated endocytosis / nuclear envelope / protein-folding chaperone binding / protease binding / vesicle / endosome / positive regulation of apoptotic process / axon / dendrite / glutamatergic synapse / negative regulation of transcription by RNA polymerase II / membrane / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Amphiphysin 2 / Amphiphysin 2, SH3 domain / Amphiphysin / BAR domain / BAR domain profile. / BAR / Arfaptin homology (AH) domain/BAR domain / BAR domain / AH/BAR domain superfamily / Variant SH3 domain ...Amphiphysin 2 / Amphiphysin 2, SH3 domain / Amphiphysin / BAR domain / BAR domain profile. / BAR / Arfaptin homology (AH) domain/BAR domain / BAR domain / 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
XENON / Myc box-dependent-interacting protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsCasal, E. / Federici, L. / Zhang, W. / Fernandez-Recio, J. / Priego, E.M. / Miguel, R.N. / Duhadaway, J.B. / Prendergast, G.C. / Luisi, B.F. / Laue, E.D.
CitationJournal: Biochemistry / Year: 2006
Title: The Crystal Structure of the BAR Domain from Human Bin1/Amphiphysin II and Its Implications for Molecular Recognition
Authors: Casal, E. / Federici, L. / Zhang, W. / Fernandez-Recio, J. / Priego, E.M. / Miguel, R.N. / Duhadaway, J.B. / Prendergast, G.C. / Luisi, B.F. / Laue, E.D.
History
DepositionDec 29, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 14, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations ...Advisory / Derived calculations / Refinement description / Version format compliance
Revision 1.3Oct 24, 2018Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / pdbx_entry_details / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity.pdbx_fragment ..._entity.pdbx_description / _entity.pdbx_fragment / _entity_name_com.name / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_seq_type / _struct_ref.pdbx_db_isoform / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq_dif.details / _struct_ref_seq_dif.pdbx_seq_db_accession_code
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Myc box-dependent-interacting protein 1
B: Myc box-dependent-interacting protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,7904
Polymers57,5272
Non-polymers2632
Water3,459192
1
A: Myc box-dependent-interacting protein 1
hetero molecules

B: Myc box-dependent-interacting protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,7904
Polymers57,5272
Non-polymers2632
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y+1/2,-z1
Buried area4630 Å2
ΔGint-39 kcal/mol
Surface area21440 Å2
MethodPISA
2
A: Myc box-dependent-interacting protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8952
Polymers28,7641
Non-polymers1311
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
B: Myc box-dependent-interacting protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8952
Polymers28,7641
Non-polymers1311
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)69.922, 59.086, 75.009
Angle α, β, γ (deg.)90.00, 117.53, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe physiological dimer is generated by applying the following to chain A: rotation: -0.90244 0.408204 0.137733 0.401865 0.682401 0.610601 0.155261 0.606381 -0.77987 translation: 34.9167, -11.5281, 9.41392

-
Components

#1: Protein Myc box-dependent-interacting protein 1 / Amphiphysin II / Amphiphysin-like protein / Box-dependent myc-interacting protein 1 / Bridging integrator 1


Mass: 28763.594 Da / Num. of mol.: 2 / Fragment: BAR domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BIN1, AMPHL / Plasmid: pET14b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O00499
#2: Chemical ChemComp-XE / XENON / Xenon


Mass: 131.293 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Xe
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 192 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSequence of the protein was based on Isoform IIB of database UNP O00499 (BIN1_HUMAN).

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.39 Å3/Da / Density % sol: 48.49 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 20% monomethylether-PEG550, 100mM Tris (pH 8), 100mM NaCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 10, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.99→27.5 Å / Num. all: 36616 / Num. obs: 36616 / % possible obs: 98.2 % / Observed criterion σ(F): 0.019 / Observed criterion σ(I): 0
Reflection shellResolution: 1.99→2.07 Å / % possible all: 84.8

-
Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.99→15 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.915 / SU B: 4.994 / SU ML: 0.138 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.202 / ESU R Free: 0.188 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27989 3653 10 %RANDOM
Rwork0.23029 ---
all0.311 32894 --
obs0.23535 32894 98.26 %-
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: 20.19 Å2
Baniso -1Baniso -2Baniso -3
1-2.72 Å20 Å2-0.35 Å2
2---0.91 Å20 Å2
3----2.13 Å2
Refinement stepCycle: LAST / Resolution: 1.99→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3206 0 2 192 3400
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0213282
X-RAY DIFFRACTIONr_bond_other_d0.0030.022885
X-RAY DIFFRACTIONr_angle_refined_deg1.6421.954417
X-RAY DIFFRACTIONr_angle_other_deg0.95736772
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8065390
X-RAY DIFFRACTIONr_chiral_restr0.1710.2475
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023640
X-RAY DIFFRACTIONr_gen_planes_other0.0080.02622
X-RAY DIFFRACTIONr_nbd_refined0.2180.2792
X-RAY DIFFRACTIONr_nbd_other0.2350.23101
X-RAY DIFFRACTIONr_nbtor_other0.0930.21873
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.3220.2148
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2330.219
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2410.2103
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2050.220
X-RAY DIFFRACTIONr_mcbond_it1.0181.51962
X-RAY DIFFRACTIONr_mcangle_it1.87923144
X-RAY DIFFRACTIONr_scbond_it2.94731320
X-RAY DIFFRACTIONr_scangle_it4.7294.51273
LS refinement shellResolution: 1.992→2.043 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.341 217
Rwork0.301 2065
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)
11.0174-1.284.59171.0335-3.482719.7886-0.10890.1790.10810.25740.0196-0.0403-0.48090.44050.08930.1926-0.1021-0.01970.21250.02660.263718.02154.110817.9641
2-0.1749-0.20270.35280.588-0.10376.5984-0.06770.04740.08380.1653-0.03090.05130.2097-0.26540.09860.1721-0.02970.00260.2410.02310.278911.20092.366722.3844
332.6351-2.495916.953741.496310.2735109.28880.3356-2.26330.06842.1274-0.1552-0.0943-0.66140.1479-0.18030.2834-0.0004-0.00030.2825-0.00010.28221.94524.610871.9234
432.990334.73892.933370.8135-12.453276.10870.09010.3148-0.82050.15630.15740.256-0.3822-0.1571-0.24750.2818-0.0006-0.00050.28260.00010.282619.2057.794580.4558
50.9917-1.6802-2.08786.551510.147130.1311-0.1817-0.33630.06130.72690.03220.41781.5064-1.06870.14960.28040.00140.00280.2794-0.0070.275414.1148-1.346858.2438
60.338-0.85632.66331.9043-3.985917.47690.17760.01410.0246-0.1677-0.0460.07360.55720.221-0.13160.1742-0.0249-0.03090.21730.01180.282714.4823-6.33297.9692
70.44872.46173.39637.289311.206218.79910.0109-0.17450.1535-0.2669-0.36090.1758-0.4093-0.7190.34990.08580.1812-0.04720.3866-0.13230.295847.3818-19.31660.9417
8-0.5135-0.5046-0.60449.16989.06069.1767-0.00840.02990.0509-0.0884-0.46340.4928-0.1155-0.5490.47170.05530.0861-0.01490.4506-0.22360.3541.1418-17.8048.5144
96.3791-10.9089-7.106921.735716.38911.0484-0.44810.4696-0.48270.772-0.42231.12320.6064-0.53540.87040.1940.01360.12840.2948-0.10990.292139.87991.309935.7121
100.16360.49380.52498.206511.185715.98490.0415-0.09580.0750.3277-0.10250.14510.5185-0.12620.0610.16530.01660.00220.2328-0.070.241249.7085-34.7449-1.5524
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A52 - 103
2X-RAY DIFFRACTION2A104 - 159
3X-RAY DIFFRACTION3A160 - 171
4X-RAY DIFFRACTION4A172 - 181
5X-RAY DIFFRACTION5A182 - 211
6X-RAY DIFFRACTION6A212 - 249
7X-RAY DIFFRACTION7B50 - 103
8X-RAY DIFFRACTION8B104 - 166
9X-RAY DIFFRACTION9B179 - 211
10X-RAY DIFFRACTION10B212 - 250

+
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