[English] 日本語
Yorodumi
- PDB-5xbf: Crystal Structure of Myo7b C-terminal MyTH4-FERM in complex with ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5xbf
TitleCrystal Structure of Myo7b C-terminal MyTH4-FERM in complex with USH1C PDZ3
Components
  • Harmonin
  • Unconventional myosin-VIIb
KeywordsMOTOR PROTEIN / PROTEIN TRANSPORT/STRUCTURAL PROTEIN / Protein complex / Molecular motor / PROTEIN TRANSPORT-STRUCTURAL PROTEIN complex
Function / homology
Function and homology information


apical cytoplasm / protein localization to microvillus / brush border assembly / regulation of microvillus length / stereocilia ankle link complex / parallel actin filament bundle assembly / equilibrioception / sensory perception of light stimulus / retinal cone cell development / stereocilium tip ...apical cytoplasm / protein localization to microvillus / brush border assembly / regulation of microvillus length / stereocilia ankle link complex / parallel actin filament bundle assembly / equilibrioception / sensory perception of light stimulus / retinal cone cell development / stereocilium tip / inner ear receptor cell stereocilium organization / sensory organ development / actin filament-based movement / inner ear auditory receptor cell differentiation / stereocilium / photoreceptor cell maintenance / myosin complex / Sensory processing of sound by outer hair cells of the cochlea / Sensory processing of sound by inner hair cells of the cochlea / inner ear morphogenesis / spectrin binding / microfilament motor activity / brush border / microvillus / actin filament bundle assembly / photoreceptor outer segment / photoreceptor inner segment / actin filament organization / sensory perception of sound / cilium / endocytosis / G2/M transition of mitotic cell cycle / actin filament binding / actin cytoskeleton / apical part of cell / protein-containing complex assembly / cell differentiation / cytoskeleton / synapse / ATP binding / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Class VII myosin, motor domain / Myosin VII, FERM domain C-lobe, repeat 1 / Myosin VII, FERM domain C-lobe, repeat 2 / Harmonin, N-terminal domain / Harmonin / MyTH4 domain / MyTH4 domain superfamily / MyTH4 domain / MyTH4 domain profile. / Domain in Myosin and Kinesin Tails ...Class VII myosin, motor domain / Myosin VII, FERM domain C-lobe, repeat 1 / Myosin VII, FERM domain C-lobe, repeat 2 / Harmonin, N-terminal domain / Harmonin / MyTH4 domain / MyTH4 domain superfamily / MyTH4 domain / MyTH4 domain profile. / Domain in Myosin and Kinesin Tails / IQ calmodulin-binding motif / Variant SH3 domain / FERM central domain / FERM/acyl-CoA-binding protein superfamily / Short calmodulin-binding motif containing conserved Ile and Gln residues. / Myosin head, motor domain / Myosin head (motor domain) / Myosin motor domain profile. / Myosin. Large ATPases. / IQ motif profile. / PDZ domain / Pdz3 Domain / IQ motif, EF-hand binding site / FERM central domain / FERM superfamily, second domain / FERM domain / FERM domain profile. / Band 4.1 domain / Band 4.1 homologues / Kinesin motor domain superfamily / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / PH-like domain superfamily / Ubiquitin-like domain superfamily / Roll / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / D-MALATE / Unconventional myosin-VIIb / Harmonin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.802 Å
AuthorsLi, J. / He, Y. / Weck, W.L. / Lu, Q. / Tyska, M.J. / Zhang, M.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Structure of Myo7b/USH1C complex suggests a general PDZ domain binding mode by MyTH4-FERM myosins.
Authors: Li, J. / He, Y. / Weck, M.L. / Lu, Q. / Tyska, M.J. / Zhang, M.
History
DepositionMar 17, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 17, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Unconventional myosin-VIIb
B: Harmonin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,7717
Polymers73,3022
Non-polymers4695
Water4,774265
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3180 Å2
ΔGint-15 kcal/mol
Surface area26610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.634, 42.537, 118.390
Angle α, β, γ (deg.)90.000, 97.510, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 2 types, 2 molecules AB

#1: Protein Unconventional myosin-VIIb


Mass: 59444.406 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 1601-2116
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MYO7B / Production host: Escherichia coli (E. coli) / References: UniProt: Q6PIF6
#2: Protein Harmonin / Antigen NY-CO-38/NY-CO-37 / Autoimmune enteropathy-related antigen AIE-75 / Protein PDZ-73 / Renal ...Antigen NY-CO-38/NY-CO-37 / Autoimmune enteropathy-related antigen AIE-75 / Protein PDZ-73 / Renal carcinoma antigen NY-REN-3 / Usher syndrome type-1C protein


Mass: 13857.638 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 428-552
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: USH1C, AIE75 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y6N9

-
Non-polymers , 4 types, 270 molecules

#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-MLT / D-MALATE / (2R)-2-HYDROXYBUTANEDIOIC ACID / 2-HYDROXY-SUCCINIC ACID


Mass: 134.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O5
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 265 / 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: 2.37 Å3/Da / Density % sol: 48.13 %
Crystal growTemperature: 299 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 8% tacsimate, pH 7.0 and 20% v/w PEG 3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9787 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 13, 2015
RadiationMonochromator: Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 63640 / % possible obs: 99.1 % / Redundancy: 3 % / Biso Wilson estimate: 26.21 Å2 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.039 / Rrim(I) all: 0.071 / Χ2: 1.548 / Net I/σ(I): 11.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.8-1.8330.4920.8720.330.5950.99799.8
1.83-1.863.10.4210.8950.2820.5091.04499.7
1.86-1.930.3480.9320.2330.4211.12699.8
1.9-1.9430.2850.9490.190.3441.17499.8
1.94-1.983.10.2380.9640.1580.2871.16999.7
1.98-2.033.10.1970.9690.1320.2381.24799.8
2.03-2.083.10.1680.9750.1110.2021.26699.6
2.08-2.1330.1390.9820.0920.1681.30399.7
2.13-2.23.10.1230.9850.0810.1471.30199.5
2.2-2.273.10.1010.9910.0670.1221.33599.6
2.27-2.353.10.0970.990.0640.1161.36199.4
2.35-2.443.10.0830.9920.0540.11.40699.5
2.44-2.553.10.0730.9930.0480.0871.38899.4
2.55-2.693.10.0620.9950.040.0741.45199.1
2.69-2.863.10.0570.9950.0370.0681.63399.2
2.86-3.083.10.0560.9950.0360.0672.24298.9
3.08-3.3930.0540.9950.0350.0652.89598.1
3.39-3.882.90.0480.9950.0320.0583.14697.6
3.88-4.8830.0390.9960.0260.0472.29297.8
4.88-5030.0310.9970.020.0361.3896.6

-
Processing

Software
NameVersionClassification
DENZOdata collection
SCALEPACKdata scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.22data extraction
DENZOdata reduction
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.802→35.293 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.62
RfactorNum. reflection% reflection
Rfree0.2107 3147 4.95 %
Rwork0.1871 --
obs0.1883 63626 99.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 106.04 Å2 / Biso mean: 37.5902 Å2 / Biso min: 15.66 Å2
Refinement stepCycle: final / Resolution: 1.802→35.293 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4583 0 31 265 4879
Biso mean--63.21 34.71 -
Num. residues----586
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114764
X-RAY DIFFRACTIONf_angle_d0.9976486
X-RAY DIFFRACTIONf_chiral_restr0.066729
X-RAY DIFFRACTIONf_plane_restr0.006826
X-RAY DIFFRACTIONf_dihedral_angle_d5.7723875
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 22

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8016-1.82970.30251590.27162680283998
1.8297-1.85970.27641260.25627482874100
1.8597-1.89180.28051290.238427882917100
1.8918-1.92620.26041330.223227272860100
1.9262-1.96320.25431460.223427362882100
1.9632-2.00330.27151470.214427382885100
2.0033-2.04680.22181380.20827642902100
2.0468-2.09440.24531370.198127482885100
2.0944-2.14680.21611330.190127652898100
2.1468-2.20490.22411360.194327422878100
2.2049-2.26970.22961490.19482751290099
2.2697-2.3430.23641520.19482750290299
2.343-2.42670.22721580.19522708286699
2.4267-2.52380.22651410.194527692910100
2.5238-2.63870.21961440.19262752289699
2.6387-2.77770.22781570.19122706286399
2.7777-2.95170.19581390.19352760289999
2.9517-3.17940.21891420.19342765290799
3.1794-3.49910.22821430.19312761290498
3.4991-4.00490.18491410.17112707284897
4.0049-5.04340.16341480.15132789293798
5.0434-35.29980.18611490.17162825297497
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)
12.09210.8232-0.65451.418-1.09452.44480.17460.1539-0.0926-0.54140.105-0.6143-0.111.0473-0.12040.6360.00040.24750.7015-0.14960.422923.32574.6425-9.126
20.5699-0.4984-0.8760.9140.99324.5760.09010.11190.0543-0.17730.0782-0.15850.09780.3109-0.1580.331-0.0323-0.00130.2385-0.01170.23598.08688.772110.5675
32.33180.0376-0.67220.5583-0.08541.26450.028-0.09270.01910.02640.007-0.0345-0.15570.0626-0.02690.2151-0.0369-0.03370.1431-0.00690.22032.425611.320247.013
46.6849-0.70871.45995.0597-0.36077.7330.0047-0.2672-1.06240.05610.0704-0.35871.3819-0.0909-0.07350.5128-0.0398-0.05130.4007-0.01410.54939.2345-14.278848.1266
52.2377-1.49240.20421.0577-0.58165.2298-0.46930.2448-0.4137-0.54390.24-0.06940.1953-0.27050.28340.4302-0.16190.03860.4251-0.0790.324334.8136-10.176740.5446
66.2324-4.0978-0.74574.86163.56695.790.08690.28690.2799-0.2081-0.0366-0.3298-0.0363-0.2943-0.00320.2129-0.1024-0.0060.31180.04670.234431.80632.290637.4175
71.46320.88670.84462.42690.04752.2206-0.5310.7409-0.5327-0.65590.2984-0.36490.49770.010.11130.336-0.1310.080.4467-0.09030.335936.5711-5.028434.5998
81.527-2.34031.13883.7776-0.9254.2715-0.08580.8948-0.3615-1.193-0.1847-0.73970.30130.67260.3130.4944-0.04850.18490.6564-0.17120.411339.9688-12.001634.4512
96.5418-6.70632.49658.1035-3.16011.40890.123-0.136-0.347-0.1608-0.01460.2844-0.00280.0322-0.16350.2241-0.0455-0.00750.23590.00420.304414.5967-0.118243.071
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1607 through 1678 )A1607 - 1678
2X-RAY DIFFRACTION2chain 'A' and (resid 1679 through 1903 )A1679 - 1903
3X-RAY DIFFRACTION3chain 'A' and (resid 1904 through 2100 )A1904 - 2100
4X-RAY DIFFRACTION4chain 'B' and (resid 432 through 444 )B432 - 444
5X-RAY DIFFRACTION5chain 'B' and (resid 445 through 465 )B445 - 465
6X-RAY DIFFRACTION6chain 'B' and (resid 466 through 484 )B466 - 484
7X-RAY DIFFRACTION7chain 'B' and (resid 485 through 527 )B485 - 527
8X-RAY DIFFRACTION8chain 'B' and (resid 528 through 538 )B528 - 538
9X-RAY DIFFRACTION9chain 'B' and (resid 539 through 552 )B539 - 552

+
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://pdbjlvh1.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