[English] 日本語
Yorodumi
- PDB-1pz8: Modulation of agrin function by alternative splicing and Ca2+ binding -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1pz8
TitleModulation of agrin function by alternative splicing and Ca2+ binding
ComponentsAgrin
KeywordsSTRUCTURAL PROTEIN / Agrin
Function / homology
Function and homology information


extracellular matrix of synaptic cleft / acetylcholine receptor regulator activity / positive regulation of synaptic assembly at neuromuscular junction / skeletal muscle acetylcholine-gated channel clustering / chondroitin sulfate binding / laminin-1 binding / sialic acid binding / neuron cell-cell adhesion / photoreceptor ribbon synapse / dystroglycan binding ...extracellular matrix of synaptic cleft / acetylcholine receptor regulator activity / positive regulation of synaptic assembly at neuromuscular junction / skeletal muscle acetylcholine-gated channel clustering / chondroitin sulfate binding / laminin-1 binding / sialic acid binding / neuron cell-cell adhesion / photoreceptor ribbon synapse / dystroglycan binding / basal part of cell / heparan sulfate proteoglycan binding / filopodium assembly / glycosaminoglycan binding / extracellular matrix binding / positive regulation of filopodium assembly / neuromuscular junction development / receptor clustering / transmembrane receptor protein tyrosine kinase activator activity / basement membrane / laminin binding / extracellular matrix / brain development / neuromuscular junction / G protein-coupled acetylcholine receptor signaling pathway / positive regulation of GTPase activity / negative regulation of neuron projection development / signaling receptor activity / heparin binding / nervous system development / actin cytoskeleton organization / cell differentiation / membrane raft / axon / glutamatergic synapse / synapse / calcium ion binding / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region / plasma membrane
Similarity search - Function
NtA (N-terminal agrin) domain / Agrin NtA domain / NtA (N-terminal agrin) domain profile. / Follistatin-like, N-terminal / Follistatin-N-terminal domain-like / Factor I / membrane attack complex / factor I membrane attack complex / Domain found in sea urchin sperm protein, enterokinase, agrin / Laminin-type EGF-like (LE) domain profile. / Laminin G domain ...NtA (N-terminal agrin) domain / Agrin NtA domain / NtA (N-terminal agrin) domain profile. / Follistatin-like, N-terminal / Follistatin-N-terminal domain-like / Factor I / membrane attack complex / factor I membrane attack complex / Domain found in sea urchin sperm protein, enterokinase, agrin / Laminin-type EGF-like (LE) domain profile. / Laminin G domain / Laminin-type EGF-like (LE) domain signature. / Laminin-type epidermal growth factor-like domai / Laminin EGF domain / Kazal-type serine protease inhibitor domain / SEA domain superfamily / Laminin-type EGF domain / SEA domain profile. / Kazal-type serine protease inhibitor domain / SEA domain / SEA domain / Laminin G domain profile. / Kazal type serine protease inhibitors / Laminin G domain / Laminin G domain / Kazal domain superfamily / Kazal domain / Kazal domain profile. / Tissue inhibitor of metalloproteinases-like, OB-fold / EGF-type aspartate/asparagine hydroxylation site / EGF-like domain / Aspartic acid and asparagine hydroxylation site. / EGF-like calcium-binding domain / Calcium-binding EGF-like domain / Epidermal growth factor-like domain. / Jelly Rolls - #200 / EGF-like domain profile. / EGF-like domain signature 2. / EGF-like domain signature 1. / EGF-like domain / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsStetefeld, J. / Alexandrescu, A.T. / Maciejewski, M.W. / Jenny, M. / Rathgeb-Szabo, K. / Schulthess, T. / Landwehr, R. / Frank, S. / Ruegg, M.A. / Kammerer, R.A.
CitationJournal: STRUCTURE / Year: 2004
Title: Modulation of agrin function by alternative splicing and Ca2+ binding.
Authors: Stetefeld, J. / Alexandrescu, A.T. / Maciejewski, M.W. / Jenny, M. / Rathgeb-Szabo, K. / Schulthess, T. / Landwehr, R. / Frank, S. / Ruegg, M.A. / Kammerer, R.A.
History
DepositionJul 10, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 13, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Remark 999 SEQUENCE the c-terminal agrin domain has alternative splice variants, we solved the structure of ... SEQUENCE the c-terminal agrin domain has alternative splice variants, we solved the structure of B11 (1pz7) and B8 with (1pz8) and without (1pz9) calcium, therefore the sequence-file conatins either 11 or 8 residues more than the so called B0-insert, the insert starts at TKS- and ends at EKA, B11:PDALDYPAEPS B8:HLSNEIPA however, not all the splice-residues are detectable in the electron density map

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Agrin
B: Agrin
C: Agrin
D: Agrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,3698
Polymers88,2084
Non-polymers1604
Water10,251569
1
A: Agrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0922
Polymers22,0521
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Agrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0922
Polymers22,0521
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Agrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0922
Polymers22,0521
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Agrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0922
Polymers22,0521
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.847, 56.556, 84.586
Angle α, β, γ (deg.)90.00, 99.75, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Agrin /


Mass: 22052.047 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Fragment: Basal Lamina Domain / Gene: AGRN / Production host: Escherichia coli (E. coli) / References: UniProt: P31696
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 569 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.05 Å3/Da / Density % sol: 40.09 %
Crystal growTemperature: 276 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 276K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, Hamburg / Beamline: BW7B / Wavelength: 1 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.35→24.8 Å / Num. obs: 29221 / % possible obs: 97.1 % / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Rsym value: 0.119 / Net I/σ(I): 11.3

-
Processing

Software
NameVersionClassification
REFMAC5refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→20 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.894 / SU B: 12.738 / SU ML: 0.309 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.689 / ESU R Free: 0.291 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26023 1479 5.1 %RANDOM
Rwork0.21778 ---
obs0.21991 27706 100 %-
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: 15.195 Å2
Baniso -1Baniso -2Baniso -3
1--1.55 Å20 Å20.04 Å2
2--0.26 Å20 Å2
3---1.3 Å2
Refinement stepCycle: LAST / Resolution: 2.35→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5485 0 4 569 6058
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0215601
X-RAY DIFFRACTIONr_bond_other_d0.0010.025080
X-RAY DIFFRACTIONr_angle_refined_deg1.5351.9467599
X-RAY DIFFRACTIONr_angle_other_deg0.829311798
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.9493700
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.24215985
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0930.2865
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026240
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021096
X-RAY DIFFRACTIONr_nbd_refined0.2470.31232
X-RAY DIFFRACTIONr_nbd_other0.2510.35137
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0490.52
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1620.5487
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0140.53
X-RAY DIFFRACTIONr_metal_ion_refined0.1120.52
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1670.345
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2810.3132
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1750.524
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.8971.53500
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.6525615
X-RAY DIFFRACTIONr_scbond_it2.2132101
X-RAY DIFFRACTIONr_scangle_it3.7314.51984
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.35→2.41 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.378 91
Rwork0.332 2078
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)
11.76620.28321.09120.77820.59951.0873-0.0178-0.0765-0.1167-0.0131-0.02870.0649-0.0514-0.0590.04650.0884-0.01790.03650.07590.02080.0747-0.62737.35937.614
22.7280.29880.6110.91990.35072.02920.0187-0.04080.00250.0699-0.03930.1165-0.0436-0.14860.02060.101-0.01420.00940.03590.03420.065930.6937.42178.882
32.1876-0.0393-0.46660.9216-0.34652.2816-0.0221-0.0633-0.02350.06620.029-0.12790.02780.1562-0.00690.0684-0.0131-0.0010.0431-0.04090.041724.687-0.36137.123
42.31090.3193-0.40191.0824-0.34821.95250.01670.0104-0.0760.0675-0.042-0.21310.01430.17030.02530.0623-0.0018-0.00930.0481-0.02240.060755.85426.72378.936
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA13 - 2913 - 29
2X-RAY DIFFRACTION1AA41 - 19841 - 198
3X-RAY DIFFRACTION2BB13 - 3013 - 30
4X-RAY DIFFRACTION2BB41 - 19841 - 198
5X-RAY DIFFRACTION3CC13 - 2913 - 29
6X-RAY DIFFRACTION3CC41 - 19841 - 198
7X-RAY DIFFRACTION4DD13 - 2913 - 29
8X-RAY DIFFRACTION4DD41 - 19841 - 198

+
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