[English] 日本語
Yorodumi
- PDB-3fb2: Crystal structure of the human brain alpha spectrin repeats 15 an... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3fb2
TitleCrystal structure of the human brain alpha spectrin repeats 15 and 16. Northeast Structural Genomics Consortium target HR5563a.
ComponentsSpectrin alpha chain, brain spectrin
KeywordsSTRUCTURAL PROTEIN / Spectrin alpha chain / brain spectrin / non-erythroid alpha chain Alpha-II spectrin / fordrin alpha chain / SPTAN1 / SPTA2_HUMAN / NESG / HR5563A / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / Actin capping / Actin-binding / Alternative splicing / Calcium / Calmodulin-binding / Cytoplasm / Cytoskeleton / Phosphoprotein / Polymorphism / SH3 domain
Function / homology
Function and homology information


spectrin / actin filament capping / Sensory processing of sound by outer hair cells of the cochlea / Interaction between L1 and Ankyrins / Sensory processing of sound by inner hair cells of the cochlea / Nephrin family interactions / RHOV GTPase cycle / cortical actin cytoskeleton / RHOU GTPase cycle / Caspase-mediated cleavage of cytoskeletal proteins ...spectrin / actin filament capping / Sensory processing of sound by outer hair cells of the cochlea / Interaction between L1 and Ankyrins / Sensory processing of sound by inner hair cells of the cochlea / Nephrin family interactions / RHOV GTPase cycle / cortical actin cytoskeleton / RHOU GTPase cycle / Caspase-mediated cleavage of cytoskeletal proteins / COPI-mediated anterograde transport / NCAM signaling for neurite out-growth / cell projection / structural constituent of cytoskeleton / specific granule lumen / microtubule cytoskeleton / extracellular vesicle / actin filament binding / tertiary granule lumen / cell junction / actin binding / actin cytoskeleton organization / RAF/MAP kinase cascade / calmodulin binding / cadherin binding / intracellular membrane-bounded organelle / calcium ion binding / Neutrophil degranulation / extracellular exosome / extracellular region / membrane / plasma membrane / cytosol
Similarity search - Function
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #60 / Alpha Spectrin, SH3 domain / EF-hand, Ca insensitive / Ca2+ insensitive EF hand / Ca2+ insensitive EF hand / Spectrin repeat / Spectrin repeat / Spectrin/alpha-actinin / Spectrin repeats / Methane Monooxygenase Hydroxylase; Chain G, domain 1 ...Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #60 / Alpha Spectrin, SH3 domain / EF-hand, Ca insensitive / Ca2+ insensitive EF hand / Ca2+ insensitive EF hand / Spectrin repeat / Spectrin repeat / Spectrin/alpha-actinin / Spectrin repeats / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / SH3 domain / EF-hand domain pair / EF-hand, calcium binding motif / Src homology 3 domains / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / EF-hand domain / EF-hand domain pair / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Spectrin alpha chain, non-erythrocytic 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsVorobiev, S.M. / Su, M. / Seetharaman, J. / Shastry, R. / Foote, E.L. / Ciccosanti, C. / Janjua, H. / Xiao, R. / Acton, T.B. / Montelione, G.T. ...Vorobiev, S.M. / Su, M. / Seetharaman, J. / Shastry, R. / Foote, E.L. / Ciccosanti, C. / Janjua, H. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal structure of the human brain alpha spectrin repeats 15 and 16.
Authors: Vorobiev, S.M. / Su, M. / Seetharaman, J. / Shastry, R. / Foote, E.L. / Ciccosanti, C. / Janjua, H. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F.
History
DepositionNov 18, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Spectrin alpha chain, brain spectrin
B: Spectrin alpha chain, brain spectrin


Theoretical massNumber of molelcules
Total (without water)51,3322
Polymers51,3322
Non-polymers00
Water5,044280
1
A: Spectrin alpha chain, brain spectrin


Theoretical massNumber of molelcules
Total (without water)25,6661
Polymers25,6661
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Spectrin alpha chain, brain spectrin


Theoretical massNumber of molelcules
Total (without water)25,6661
Polymers25,6661
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.610, 96.376, 111.145
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Detailsmonomer according to aggregation screening

-
Components

#1: Protein Spectrin alpha chain, brain spectrin / Spectrin / non-erythroid alpha chain / Alpha-II spectrin / Fodrin alpha chain


Mass: 25665.805 Da / Num. of mol.: 2 / Fragment: Repeats 15 and 16
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SPTA2, SPTAN1 / Plasmid: pET 14-15C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) +Magic / References: UniProt: Q13813
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 280 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.42 Å3/Da / Density % sol: 64.06 %
Crystal growTemperature: 277 K / Method: microbatch crystallization under oil / pH: 5
Details: 12% PEG 20000, 0.1M magnesium sulfate, 0.1M sodium acetate, pH 5.0, microbatch crystallization under oil, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97905 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 11, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97905 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 60976 / Num. obs: 58903 / % possible obs: 96.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6 % / Biso Wilson estimate: 19.6 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 30.8
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.318 / Mean I/σ(I) obs: 6.03 / Num. unique all: 6075 / % possible all: 99.2

-
Processing

Software
NameVersionClassification
HKL-2000data collection
SnBphasing
RESOLVEmodel building
CNS1.2refinement
HKL-2000data reduction
SCALEPACKdata scaling
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.3→36.41 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 412014.45 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.248 2399 4.9 %RANDOM
Rwork0.219 ---
obs0.219 49428 81.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 36.8762 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 47.4 Å2
Baniso -1Baniso -2Baniso -3
1--7.06 Å20 Å20 Å2
2--30.72 Å20 Å2
3----23.66 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.23 Å
Refinement stepCycle: LAST / Resolution: 2.3→36.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3179 0 0 280 3459
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg0.9
X-RAY DIFFRACTIONc_dihedral_angle_d19.1
X-RAY DIFFRACTIONc_improper_angle_d0.67
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.261 261 4.2 %
Rwork0.247 5908 -
obs--61.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

+
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