[English] 日本語
Yorodumi
- PDB-3tad: Crystal Structure of the Liprin-alpha/Liprin-beta complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3tad
TitleCrystal Structure of the Liprin-alpha/Liprin-beta complex
Components
  • Liprin-alpha-2
  • Liprin-beta-1
KeywordsPROTEIN BINDING
Function / homology
Function and homology information


structural constituent of presynapse / Receptor-type tyrosine-protein phosphatases / dense core granule cytoskeletal transport / Receptor-type tyrosine-protein phosphatases / Acetylcholine Neurotransmitter Release Cycle / Serotonin Neurotransmitter Release Cycle / postsynaptic specialization / regulation of dendritic spine development / Dopamine Neurotransmitter Release Cycle / Norepinephrine Neurotransmitter Release Cycle ...structural constituent of presynapse / Receptor-type tyrosine-protein phosphatases / dense core granule cytoskeletal transport / Receptor-type tyrosine-protein phosphatases / Acetylcholine Neurotransmitter Release Cycle / Serotonin Neurotransmitter Release Cycle / postsynaptic specialization / regulation of dendritic spine development / Dopamine Neurotransmitter Release Cycle / Norepinephrine Neurotransmitter Release Cycle / Glutamate Neurotransmitter Release Cycle / regulation of dendritic spine morphogenesis / regulation of synaptic vesicle exocytosis / neuromuscular junction development / presynaptic active zone / cell-matrix adhesion / synapse organization / synaptic vesicle / presynaptic membrane / dendritic spine / axon / glutamatergic synapse / cell surface / extracellular exosome / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Liprin-beta, SAM domain repeat 1 / Liprin-beta, SAM domain repeat 2 / Liprin-beta, SAM domain repeat 3 / Liprin-alpha, SAM domain repeat 1 / Liprin-alpha, SAM domain repeat 2 / Liprin-alpha, SAM domain repeat 3 / LAR-interacting protein, Liprin / Transcription Factor, Ets-1 / SAM domain (Sterile alpha motif) / SAM domain (Sterile alpha motif) ...Liprin-beta, SAM domain repeat 1 / Liprin-beta, SAM domain repeat 2 / Liprin-beta, SAM domain repeat 3 / Liprin-alpha, SAM domain repeat 1 / Liprin-alpha, SAM domain repeat 2 / Liprin-alpha, SAM domain repeat 3 / LAR-interacting protein, Liprin / Transcription Factor, Ets-1 / SAM domain (Sterile alpha motif) / SAM domain (Sterile alpha motif) / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / DNA polymerase; domain 1 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Liprin-alpha-2 / Liprin-beta-1
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.9 Å
AuthorsWei, Z. / Zheng, S. / Yu, C. / Zhang, M.
CitationJournal: Mol.Cell / Year: 2011
Title: Liprin-mediated large signaling complex organization revealed by the liprin-alpha/CASK and liprin-alpha/liprin-beta complex structures
Authors: Wei, Z. / Zheng, S. / Spangler, S.A. / Yu, C. / Hoogenraad, C.C. / Zhang, M.
History
DepositionAug 4, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 12, 2011Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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 / _struct_ref_seq_dif.details / _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: Liprin-alpha-2
B: Liprin-alpha-2
C: Liprin-beta-1
D: Liprin-beta-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,7749
Polymers129,3144
Non-polymers4605
Water23413
1
A: Liprin-alpha-2
C: Liprin-beta-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,8414
Polymers64,6572
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Liprin-alpha-2
D: Liprin-beta-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,9335
Polymers64,6572
Non-polymers2763
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)141.880, 141.880, 181.059
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A
12D
22C

NCS domain segments:

Refine code: 5

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111GLNGLNSERSERBB871 - 96612 - 107
211GLNGLNSERSERAA871 - 96612 - 107
121TYRTYRLEULEUBB1016 - 1177120 - 281
221TYRTYRLEULEUAA1016 - 1177120 - 281
112LYSLYSGLYGLYDD608 - 62120 - 33
212LYSLYSGLYGLYCC608 - 62120 - 33
122SERSERSERSERDD633 - 66945 - 81
222SERSERSERSERCC633 - 66945 - 81
132THRTHRLEULEUDD759 - 853171 - 265
232THRTHRLEULEUCC759 - 853171 - 265
142THRTHRARGARGDD673 - 75085 - 162
242THRTHRARGARGCC673 - 75085 - 162

NCS ensembles :
ID
1
2

-
Components

#1: Protein Liprin-alpha-2 / Protein tyrosine phosphatase receptor type f polypeptide-interacting protein alpha-2 / PTPRF- ...Protein tyrosine phosphatase receptor type f polypeptide-interacting protein alpha-2 / PTPRF-interacting protein alpha-2


Mass: 34349.305 Da / Num. of mol.: 2 / Fragment: UNP residues 866-975, 1113-1193
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPFIA2 / Plasmid: pET32a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O75334
#2: Protein Liprin-beta-1 / Protein tyrosine phosphatase receptor type f polypeptide-interacting protein-binding protein 1 / ...Protein tyrosine phosphatase receptor type f polypeptide-interacting protein-binding protein 1 / PTPRF-interacting protein-binding protein 1


Mass: 30307.514 Da / Num. of mol.: 2 / Fragment: UNP residues 593-853
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ppfibp1 / Plasmid: pET32a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8C8U0
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 4.07 Å3/Da / Density % sol: 69.76 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 3-5% PEG8000, 0.15M NaCl, 0.1M Bis-Tris buffer, pH 6.0, vapor diffusion, hanging drop, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.98 Å
DetectorDetector: CCD / Date: Apr 1, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 45715 / % possible obs: 99.5 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.068

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
PHASERphasing
REFMAC5.5.0072refinement
PDB_EXTRACT3.1data extraction
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→44.98 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.919 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 29.671 / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.335 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2583 2263 5 %RANDOM
Rwork0.2136 ---
obs0.2159 45029 98.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 229.82 Å2 / Biso mean: 102.4018 Å2 / Biso min: 16 Å2
Baniso -1Baniso -2Baniso -3
1-1.09 Å20.54 Å2-0 Å2
2--1.09 Å2-0 Å2
3----1.63 Å2
Refinement stepCycle: LAST / Resolution: 2.9→44.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8113 0 30 13 8156
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0218318
X-RAY DIFFRACTIONr_angle_refined_deg1.2641.95511291
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.14351027
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.71223.958384
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.493151409
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3171559
X-RAY DIFFRACTIONr_chiral_restr0.0880.21268
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0216264
X-RAY DIFFRACTIONr_mcbond_it1.59925136
X-RAY DIFFRACTIONr_mcangle_it2.97738196
X-RAY DIFFRACTIONr_scbond_it4.67143182
X-RAY DIFFRACTIONr_scangle_it7.35863094
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1B1032medium positional0.210.5
2D895medium positional0.30.5
1B982loose positional0.455
2D866loose positional0.475
1B1032medium thermal0.462
2D895medium thermal3.262
1B982loose thermal0.7410
2D866loose thermal4.110
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.391 148 -
Rwork0.271 3093 -
all-3241 -
obs--96.66 %
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)
12.30962.9817-1.33688.0342-3.17241.9968-0.04640.1535-0.31570.64280.13580.97420.1238-0.4381-0.08940.7257-0.31420.24880.4779-0.11040.7872-29.8165-41.847768.9404
22.2252.03531.25857.29722.54612.67740.01170.14330.3540.56710.2794-1.5315-0.2910.6684-0.29110.5797-0.31330.05480.5231-0.11890.923949.78737.058366.0934
32.98080.04220.00493.61920.53553.93110.1910.32650.5106-0.3986-0.1421-0.1671-0.8392-0.2096-0.04880.30830.09650.06350.25770.03350.1016-2.70728.878442.7732
42.0570.81690.33023.65181.26373.49060.12240.0902-0.24640.01870.05-0.08470.29910.0951-0.17240.08230.0724-0.0220.2052-0.02830.040218.6047-12.409842.3751
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A870 - 1177
2X-RAY DIFFRACTION2B871 - 1177
3X-RAY DIFFRACTION3C602 - 853
4X-RAY DIFFRACTION4D601 - 853

+
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