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- PDB-6m3p: Crystal structure of AnkG/beta2-spectrin complex -

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Basic information

Entry
Database: PDB / ID: 6m3p
TitleCrystal structure of AnkG/beta2-spectrin complex
Components
  • Ankyrin-3
  • Spectrin beta chain, non-erythrocytic 1
KeywordsSTRUCTURAL PROTEIN / PROTEIN BINDING
Function / homology
Function and homology information


Interaction between L1 and Ankyrins / regulation of protein targeting / positive regulation of sodium ion import across plasma membrane / positive regulation of cell communication by electrical coupling / positive regulation of membrane depolarization during cardiac muscle cell action potential / maintenance of protein location in plasma membrane / regulation of SMAD protein signal transduction / RHOV GTPase cycle / membrane assembly / NCAM signaling for neurite out-growth ...Interaction between L1 and Ankyrins / regulation of protein targeting / positive regulation of sodium ion import across plasma membrane / positive regulation of cell communication by electrical coupling / positive regulation of membrane depolarization during cardiac muscle cell action potential / maintenance of protein location in plasma membrane / regulation of SMAD protein signal transduction / RHOV GTPase cycle / membrane assembly / NCAM signaling for neurite out-growth / central nervous system formation / RHOU GTPase cycle / protein localization to axon / spectrin / clustering of voltage-gated sodium channels / spectrin-associated cytoskeleton / establishment or maintenance of microtubule cytoskeleton polarity / regulation of potassium ion transport / COPI-mediated anterograde transport / cuticular plate / magnesium ion homeostasis / positive regulation of membrane potential / RAF/MAP kinase cascade / negative regulation of delayed rectifier potassium channel activity / plasma membrane organization / channel activator activity / phosphorylation-dependent protein binding / maintenance of protein location in cell / paranode region of axon / positive regulation of homotypic cell-cell adhesion / positive regulation of sodium ion transport / actin filament capping / regulation of modification of postsynaptic structure / negative regulation of endocytosis / axon initial segment / costamere / anterograde axonal transport / cellular response to magnesium ion / Golgi to plasma membrane protein transport / node of Ranvier / M band / ankyrin binding / spectrin binding / neuromuscular junction development / cortical cytoskeleton / axon development / response to immobilization stress / mitotic cytokinesis / intercalated disc / axolemma / sodium channel regulator activity / lateral plasma membrane / positive regulation of protein targeting to membrane / bicellular tight junction / neuronal action potential / cytoskeletal protein binding / T-tubule / axon cytoplasm / positive regulation of interleukin-2 production / endomembrane system / axonogenesis / axon guidance / basal plasma membrane / sarcoplasmic reticulum / central nervous system development / protein localization to plasma membrane / positive regulation of protein localization to plasma membrane / establishment of protein localization / positive regulation of non-canonical NF-kappaB signal transduction / synapse organization / sarcolemma / phospholipid binding / neuromuscular junction / structural constituent of cytoskeleton / Z disc / actin binding / actin cytoskeleton organization / GTPase binding / protein-macromolecule adaptor activity / basolateral plasma membrane / transmembrane transporter binding / postsynaptic membrane / RNA polymerase II-specific DNA-binding transcription factor binding / cytoskeleton / lysosome / neuron projection / calmodulin binding / postsynapse / postsynaptic density / cadherin binding / axon / synapse / dendrite / positive regulation of gene expression / regulation of transcription by RNA polymerase II / protein-containing complex binding / nucleolus / glutamatergic synapse / cell surface / signal transduction
Similarity search - Function
Immunoglobulin-like - #2660 / Ankyrin-3, death domain / Chondroitinase Ac; Chain A, domain 3 - #30 / Pleckstrin homology domain, spectrin-type / Pleckstrin homology domain 9 / Pleckstrin homology domain / Spectrin, beta subunit / Ankyrin, UPA domain / UPA domain / : ...Immunoglobulin-like - #2660 / Ankyrin-3, death domain / Chondroitinase Ac; Chain A, domain 3 - #30 / Pleckstrin homology domain, spectrin-type / Pleckstrin homology domain 9 / Pleckstrin homology domain / Spectrin, beta subunit / Ankyrin, UPA domain / UPA domain / : / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #60 / Chondroitinase Ac; Chain A, domain 3 / Domain present in ZO-1 and Unc5-like netrin receptors / ZU5 domain / ZU5 domain / ZU5 domain profile. / Spectrin repeat / Spectrin repeat / Ankyrin repeats (many copies) / Actinin-type actin-binding domain signature 1. / Actinin-type actin-binding domain signature 2. / Actinin-type actin-binding domain, conserved site / Spectrin/alpha-actinin / Spectrin repeats / Death domain profile. / DEATH domain, found in proteins involved in cell death (apoptosis). / Death domain / Death domain / Calponin homology domain / Calponin homology (CH) domain / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. / Death-like domain superfamily / Ankyrin repeat / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / PH-like domain superfamily / Up-down Bundle / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Ankyrin-3 / Spectrin beta chain, non-erythrocytic 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.312 Å
AuthorsLi, J. / Chen, K. / Zhu, R. / Zhang, M.
Funding support Hong Kong, 1items
OrganizationGrant numberCountry
The University Grants Committee, Research Grants Council (RGC)16100517 Hong Kong
CitationJournal: J.Mol.Biol. / Year: 2020
Title: Structural Basis Underlying Strong Interactions between Ankyrins and Spectrins.
Authors: Li, J. / Chen, K. / Zhu, R. / Zhang, M.
History
DepositionMar 4, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 13, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: Ankyrin-3
A: Spectrin beta chain, non-erythrocytic 1
C: Ankyrin-3
B: Spectrin beta chain, non-erythrocytic 1


Theoretical massNumber of molelcules
Total (without water)183,2534
Polymers183,2534
Non-polymers00
Water00
1
E: Ankyrin-3
A: Spectrin beta chain, non-erythrocytic 1


Theoretical massNumber of molelcules
Total (without water)91,6272
Polymers91,6272
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1870 Å2
ΔGint-7 kcal/mol
Surface area37590 Å2
MethodPISA
2
C: Ankyrin-3
B: Spectrin beta chain, non-erythrocytic 1


Theoretical massNumber of molelcules
Total (without water)91,6272
Polymers91,6272
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1890 Å2
ΔGint-7 kcal/mol
Surface area37270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.277, 66.305, 160.926
Angle α, β, γ (deg.)99.470, 99.780, 100.870
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
12(chain C and (resid 960 through 1125 or (resid 1126...
22(chain E and (resid 960 through 1040 or (resid 1041...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ALAALATHRTHRchain AAB11 - 32011 - 320
211ALAALATHRTHRchain BBD11 - 32011 - 320
112VALVALLYSLYS(chain C and (resid 960 through 1125 or (resid 1126...CC960 - 112510 - 175
122GLNGLNGLUGLU(chain C and (resid 960 through 1125 or (resid 1126...CC1126 - 1127176 - 177
132VALVALHISHIS(chain C and (resid 960 through 1125 or (resid 1126...CC960 - 142210 - 473
142VALVALHISHIS(chain C and (resid 960 through 1125 or (resid 1126...CC960 - 142210 - 473
152VALVALHISHIS(chain C and (resid 960 through 1125 or (resid 1126...CC960 - 142210 - 473
162VALVALHISHIS(chain C and (resid 960 through 1125 or (resid 1126...CC960 - 142210 - 473
212VALVALPHEPHE(chain E and (resid 960 through 1040 or (resid 1041...EA960 - 104010 - 90
222LEULEULEULEU(chain E and (resid 960 through 1040 or (resid 1041...EA104191

NCS ensembles :
ID
1
2

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Components

#1: Protein Ankyrin-3 / ANK-3 / Ankyrin-G


Mass: 54560.531 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Ank3 / Production host: Escherichia coli (E. coli) / References: UniProt: O70511
#2: Protein Spectrin beta chain, non-erythrocytic 1 / Beta-II spectrin / Embryonic liver fodrin / Fodrin beta chain


Mass: 37066.059 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Sptbn1, Elf, Spnb-2, Spnb2, Sptb2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q62261

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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: 3.66 Å3/Da / Density % sol: 66.37 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 7.5
Details: 10% w/v polyethylene glycol 6,000, 5% v/v (+/-)-2-methyl-2,4-pentanediol and 0.1 M HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 3.3→50 Å / Num. obs: 37513 / % possible obs: 97.7 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.112 / Rpim(I) all: 0.088 / Rrim(I) all: 0.131 / Χ2: 0.554 / Net I/σ(I): 2.6 / Num. measured all: 103394
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Num. unique obsCC1/2Rpim(I) allΧ2% possible allRmerge(I) obsRrim(I) all
3.3-3.362.518150.5660.8910.4197.7
3.36-3.422.618690.6480.7450.41797.5
3.42-3.482.719620.6960.640.44897.70.898
3.48-3.552.517970.7910.4860.42297.40.6650.829
3.55-3.632.519130.8460.4160.43897.50.5650.706
3.63-3.722.718500.9140.3160.42297.30.4510.554
3.72-3.812.918940.9260.2980.43797.90.4310.527
3.81-3.912.918640.7230.2650.46997.10.3770.464
3.91-4.032.918480.9710.1840.4297.50.2720.33
4.03-4.162.919450.9790.1480.44497.80.2160.263
4.16-4.312.918170.9820.1240.43197.20.1840.223
4.31-4.482.918680.9860.0940.40796.80.1390.169
4.48-4.682.919200.9920.070.40897.20.1020.125
4.68-4.932.817990.9930.0670.41796.70.0970.119
4.93-5.242.818630.9930.0590.38596.70.0840.104
5.24-5.642.718660.9880.0670.51696.60.0950.117
5.64-6.212.518720.9890.0650.40198.20.0880.11
6.21-7.12.619110.9890.050.48699.40.0690.086
7.1-8.942.819290.9960.0270.52399.50.0390.047
8.94-50319110.8020.0352.43399.60.0430.056

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Processing

Software
NameVersionClassification
PHENIXv1.15.2refinement
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4D8O, 3KBT

4d8o

3kbt


Resolution: 3.312→44.995 Å / SU ML: 0.55 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 37.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2951 1723 4.69 %
Rwork0.2545 35004 -
obs0.2563 36727 95.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 221.74 Å2 / Biso mean: 107.5895 Å2 / Biso min: 36.44 Å2
Refinement stepCycle: final / Resolution: 3.312→44.995 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10198 0 0 0 10198
Num. residues----1450
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1806X-RAY DIFFRACTION3.522TORSIONAL
12B1806X-RAY DIFFRACTION3.522TORSIONAL
21C2506X-RAY DIFFRACTION3.522TORSIONAL
22E2506X-RAY DIFFRACTION3.522TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.312-3.40950.40381450.394234378
3.4095-3.51950.48991360.3613290294
3.5195-3.64520.4041330.3194290895
3.6452-3.79110.37011550.3069296297
3.7911-3.96350.35441690.278291796
3.9635-4.17240.34111610.2586298597
4.1724-4.43360.29821810.2416295197
4.4336-4.77550.27651570.205293197
4.7755-5.25540.22071120.2141297396
5.2554-6.01440.32751230.2667304697
6.0144-7.57160.3305920.2705307899
7.5716-44.9950.19931590.2171300899

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