[English] 日本語
Yorodumi
- PDB-4d7y: Crystal structure of mouse C1QL1 globular domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4d7y
TitleCrystal structure of mouse C1QL1 globular domain
ComponentsC1Q-RELATED FACTOR
KeywordsSIGNALING PROTEIN
Function / homology
Function and homology information


climbing fiber / regulation of synapse pruning / motor learning / cerebellar climbing fiber to Purkinje cell synapse / maintenance of synapse structure / collagen trimer / neuron remodeling / synaptic cleft / presynapse / signaling receptor binding / cytoplasm
Similarity search - Function
C1q domain / C1q domain / C1q domain profile. / Complement component C1q domain. / Jelly Rolls - #40 / Tumour necrosis factor-like domain superfamily / Collagen triple helix repeat / Collagen triple helix repeat (20 copies) / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / NICKEL (II) ION / C1q-related factor
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.44 Å
AuthorsKakegawa, W. / Mitakidis, N. / Miura, E. / Abe, M. / Matsuda, K. / Takeo, Y. / Kohda, K. / Motohashi, J. / Takahashi, A. / Nagao, S. ...Kakegawa, W. / Mitakidis, N. / Miura, E. / Abe, M. / Matsuda, K. / Takeo, Y. / Kohda, K. / Motohashi, J. / Takahashi, A. / Nagao, S. / Muramatsu, S. / Watanabe, M. / Sakimura, K. / Aricescu, A.R. / Yuzaki, M.
CitationJournal: Neuron / Year: 2015
Title: Anterograde C1Ql1 Signaling is Required in Order to Determine and Maintain a Single-Winner Climbing Fiber in the Mouse Cerebellum
Authors: Kakegawa, W. / Mitakidis, N. / Miura, E. / Abe, M. / Matsuda, K. / Takeo, Y. / Kohda, K. / Motohashi, J. / Takahashi, A. / Nagao, S. / Muramatsu, S. / Watanabe, M. / Sakimura, K. / Aricescu, A.R. / Yuzaki, M.
History
DepositionDec 1, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 28, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 4, 2015Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _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: C1Q-RELATED FACTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4518
Polymers16,0141
Non-polymers4377
Water1,53185
1
A: C1Q-RELATED FACTOR
hetero molecules

A: C1Q-RELATED FACTOR
hetero molecules

A: C1Q-RELATED FACTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,35324
Polymers48,0413
Non-polymers1,31221
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_565-x+y,-x+1,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
Buried area8150 Å2
ΔGint-183.8 kcal/mol
Surface area11560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.080, 68.080, 65.910
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-1259-

CD

21A-1260-

CD

31A-1261-

NI

41A-1262-

NI

51A-1263-

CL

61A-1265-

CL

71A-2034-

HOH

81A-2045-

HOH

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein C1Q-RELATED FACTOR / C1Q AND TUMOR NECROSIS FACTOR-RELATED PROTEIN 14 / C1Q/TNF-R ELATED PROTEIN 14 / CTRP14 / ...C1Q AND TUMOR NECROSIS FACTOR-RELATED PROTEIN 14 / C1Q/TNF-R ELATED PROTEIN 14 / CTRP14 / COMPLEMENT COMPONENT 1Q SUBCOMPONENT-LIKE 1 / C1QL1


Mass: 16013.554 Da / Num. of mol.: 1 / Fragment: C1Q, UNP RESIDUES 125-258
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Cell: NEURON / Organ: BRAIN / Cell line (production host): HEK-293T / Production host: HOMO SAPIENS (human) / References: UniProt: O88992

-
Non-polymers , 5 types, 92 molecules

#2: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cd
#3: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 85 / Source method: isolated from a natural source / Formula: H2O

-
Details

Sequence detailsETG AT THE N-TERMINUS AND GTKHHHHHH AT THE C-TERMINUS ORIGINATE FROM THE EXPRESSION VECTOR.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.84 Å3/Da / Density % sol: 33.12 % / Description: NONE
Crystal growpH: 4.5
Details: 0.02M NICKEL(II) CHLORIDE HEXAHYDRATE, 0.02M MAGNESIUM CHLORIDE HEXAHYDRATE, 0.02M CADMIUM CHLORIDE HYDRATE, 0.1M SODIUM ACETATE TRIHYDRATE PH 4.5, 24% W/V POLYETHYLENE GLYCOL, MONOMETHYL ETHER 2,000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97625
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 21, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.44→43.94 Å / Num. obs: 20630 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 7.6 % / Biso Wilson estimate: 13.65 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 16.9
Reflection shellResolution: 1.44→1.48 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.88 / Mean I/σ(I) obs: 2 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1C28

1c28


Resolution: 1.44→34.04 Å / SU ML: 0.13 / σ(F): 1.99 / Phase error: 17.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1693 1025 5 %
Rwork0.1401 --
obs0.1415 20628 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.44→34.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1009 0 7 85 1101
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061059
X-RAY DIFFRACTIONf_angle_d1.0961440
X-RAY DIFFRACTIONf_dihedral_angle_d11.756373
X-RAY DIFFRACTIONf_chiral_restr0.049149
X-RAY DIFFRACTIONf_plane_restr0.004191
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4401-1.5160.2551560.20542800X-RAY DIFFRACTION100
1.516-1.6110.20931640.17832805X-RAY DIFFRACTION100
1.611-1.73540.20051600.15392767X-RAY DIFFRACTION100
1.7354-1.910.15131270.13872790X-RAY DIFFRACTION100
1.91-2.18630.16081280.12942847X-RAY DIFFRACTION100
2.1863-2.75440.18491360.14172803X-RAY DIFFRACTION100
2.7544-34.04950.14581540.12722791X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -2.5486 Å / Origin y: 27.5958 Å / Origin z: 7.7109 Å
111213212223313233
T0.0955 Å20.0015 Å20.0054 Å2-0.0907 Å20.0032 Å2--0.1004 Å2
L0.3112 °20.1305 °20.162 °2-0.444 °20.0483 °2--0.1449 °2
S-0.0096 Å °-0.0172 Å °-0.0566 Å °0.0057 Å °0.0191 Å °0.0235 Å °0.0637 Å °-0.0081 Å °-0.0001 Å °
Refinement TLS groupSelection details: CHAIN 'A' AND (RESID 128 THROUGH 258 )

+
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