[English] 日本語
Yorodumi
- PDB-5ybz: High resolution structure of complement C1q-like protein 3 C1q domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ybz
TitleHigh resolution structure of complement C1q-like protein 3 C1q domain
ComponentsComplement C1q-like protein 3
KeywordsSIGNALING PROTEIN
Function / homology
Function and homology information


trans-synaptic signaling, modulating synaptic transmission / postsynaptic density assembly / maintenance of synapse structure / neurotransmitter receptor localization to postsynaptic specialization membrane / regulation of synapse organization / synaptic cleft / hippocampal mossy fiber to CA3 synapse / synapse / glutamatergic synapse / : ...trans-synaptic signaling, modulating synaptic transmission / postsynaptic density assembly / maintenance of synapse structure / neurotransmitter receptor localization to postsynaptic specialization membrane / regulation of synapse organization / synaptic cleft / hippocampal mossy fiber to CA3 synapse / synapse / glutamatergic synapse / : / extracellular region / identical protein binding
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 ...: / 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
Complement C1q-like protein 3
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.711 Å
AuthorsLiu, H. / Li, Z. / Xu, F.
CitationJournal: To Be Published
Title: High resolution structure of complement C1q-like protein 3 C1q domain
Authors: Liu, H. / Li, Z. / Xu, F.
History
DepositionSep 5, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 3, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr3_auth_asym_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.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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.ptnr2_auth_asym_id / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Complement C1q-like protein 3
C: Complement C1q-like protein 3
D: Complement C1q-like protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,45918
Polymers45,3353
Non-polymers1,12415
Water6,053336
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8270 Å2
ΔGint-166 kcal/mol
Surface area14580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.027, 79.213, 87.495
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 1 types, 3 molecules ACD

#1: Protein Complement C1q-like protein 3 / C1q and tumor necrosis factor-related protein 13 / CTRP13 / Gliacolin


Mass: 15111.691 Da / Num. of mol.: 3 / Fragment: UNP residues 125-255
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: C1ql3, C1ql, Ctrp13 / Production host: Homo sapiens (human) / References: UniProt: Q9ESN4

-
Non-polymers , 6 types, 351 molecules

#2: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Ca
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 336 / 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: 2.1 Å3/Da / Density % sol: 41.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: ammonium sulfate, sodium citrate, manganese chloride

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BSRF / Beamline: 3W1A / Wavelength: 0.9792 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Oct 12, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.711→50 Å / Num. obs: 40768 / % possible obs: 99.8 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.076 / Χ2: 1.122 / Net I/σ(I): 26.5
Reflection shellResolution: 1.711→1.76 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.457 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 1976 / Χ2: 0.919 / % possible all: 98.1

-
Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.711→22.074 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1865 2041 5.01 %
Rwork0.1519 --
obs0.1537 40699 98.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.711→22.074 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3152 0 56 336 3544
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093322
X-RAY DIFFRACTIONf_angle_d1.0234513
X-RAY DIFFRACTIONf_dihedral_angle_d18.491155
X-RAY DIFFRACTIONf_chiral_restr0.076457
X-RAY DIFFRACTIONf_plane_restr0.007593
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.711-1.75080.32271210.24532076X-RAY DIFFRACTION81
1.7508-1.79460.231220.19992578X-RAY DIFFRACTION100
1.7946-1.84310.20541300.17142583X-RAY DIFFRACTION100
1.8431-1.89730.23191380.15982551X-RAY DIFFRACTION100
1.8973-1.95850.20031490.16142578X-RAY DIFFRACTION100
1.9585-2.02840.18221510.14762578X-RAY DIFFRACTION100
2.0284-2.10960.20121260.14432578X-RAY DIFFRACTION100
2.1096-2.20550.18441330.14842596X-RAY DIFFRACTION100
2.2055-2.32170.19211250.14872613X-RAY DIFFRACTION100
2.3217-2.4670.17871280.15392610X-RAY DIFFRACTION100
2.467-2.65710.19521260.15312627X-RAY DIFFRACTION100
2.6571-2.9240.17651600.15172589X-RAY DIFFRACTION100
2.924-3.34580.17031540.14172633X-RAY DIFFRACTION100
3.3458-4.21060.1721360.12922677X-RAY DIFFRACTION100
4.2106-22.0760.17051420.15872791X-RAY DIFFRACTION100
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)
12.3333-1.76020.85265.30620.87481.23860.04090.1591-0.3872-0.3907-0.0333-0.11160.3655-0.05870.03140.2515-0.0410.0680.1298-0.01850.1958-12.2763-13.6943-0.6941
24.3273-0.56322.19263.1798-0.70215.9765-0.0691-0.0108-0.09610.35470.01120.4992-0.2117-0.33050.04710.11560.00780.05080.14880.0070.1571-20.56616.173410.0383
32.281-0.84140.8513.7097-4.255.38930.0439-0.0484-0.114-0.13180.13130.3360.1705-0.2068-0.14340.0896-0.04-0.0050.1438-0.01310.1708-20.4051-7.01564.6708
41.0085-0.04780.25674.29-0.80640.8158-0.0152-0.0534-0.02550.0834-0.02980.0622-0.012-0.07570.04190.0592-0.00830.0180.0939-0.00390.0725-10.57661.29859.7818
55.3811.3869-1.08645.0807-3.5626.8829-0.0483-0.309-0.01180.4384-0.352-0.29270.09690.25590.3720.0974-0.0044-0.00940.1281-0.02230.059-5.1464.171414.6109
61.5469-2.12920.41993.7744-1.35241.03010.032-0.01030.1243-0.0955-0.0798-0.15790.0140.01310.05020.0624-0.0047-0.01950.086-0.00650.0808-7.057.8276.5302
71.68021.045-0.32233.9288-0.89922.43230.0516-0.1438-0.11470.5785-0.11580.15140.0032-0.26450.05610.1216-0.02850.0360.16010.00250.089-12.818-6.200614.4073
80.7612-0.0155-0.0834.02490.50191.699-0.060.0163-0.06560.03840.03340.03150.027-0.09130.00440.037-0.03160.01470.1153-0.00430.0855-13.13510.08243.6748
92.9014-0.18581.35256.7543-0.00852.4215-0.0810.103-0.7241-0.20450.1449-0.19040.5864-0.1295-0.05210.2824-0.03980.07340.1603-0.06340.2209-0.3135-8.1146-11.7884
104.607-1.04451.68125.85270.62645.7226-0.02170.40120.278-0.4874-0.0121-0.0467-0.095-0.1420.01140.1663-0.02610.00990.16910.02630.0615-3.419111.7479-17.3399
110.45030.32510.35630.35410.26540.93-0.23090.2514-0.2316-0.1097-0.088-0.02950.3907-0.1527-0.75670.3039-0.09080.0940.2169-0.17790.0784-2.8154-4.1397-17.9896
121.5205-0.0377-0.10253.09931.0211.3933-0.0510.1890.1155-0.320.0364-0.0009-0.0248-0.0974-0.00060.0983-0.0138-0.01140.12890.00490.065-8.45648.3467-8.9324
133.3995-0.8384-1.00592.8781-0.38473.32330.08590.2933-0.0492-0.1891-0.03970.33630.2416-0.2840.06430.07280.0122-0.0370.12070.02190.0764-14.52178.6967-6.5229
149.306-5.8726-4.13913.70622.59915.56240.1849-0.01920.7319-0.15240.0412-0.2299-0.2213-0.0343-0.23030.11220.00030.00080.1194-0.00770.1763-2.359522.7835-2.1908
151.12520.1097-0.12321.84710.44981.059-0.18560.3078-0.0764-0.25560.11750.00450.2139-0.11980.01590.1481-0.045-0.00070.1494-0.03090.0768-6.28582.0278-10.4547
161.7426-1.5970.11533.6951-0.92194.42290.12570.0825-0.5842-0.4087-0.41830.10890.5847-0.31630.22720.1746-0.0060.03950.1553-0.00790.33223.279-14.21594.4186
177.58471.4514-1.85763.301-2.44172.46320.2628-0.6090.38190.7643-0.1923-0.5043-0.62970.4962-0.06420.2826-0.049-0.10090.23150.00240.266812.35825.794212.3391
181.376-0.3479-1.33280.09150.43014.0329-0.1353-0.1658-0.28460.14220.035-0.1840.36410.25820.09660.14610.0295-0.0230.13440.05220.297810.9081-8.80297.0511
191.3306-0.0951-0.21971.0862-0.78140.62950.0834-0.0127-0.0620.0757-0.1071-0.3061-0.08230.0416-0.01660.05880.00040.0020.0965-0.00170.12767.63886.53251.2683
203.16631.51451.44123.0981-2.04233.79430.0191-0.19370.28880.005-0.06780.1229-0.4224-0.086-0.07580.0539-0.04260.00660.1315-0.0060.15015.766614.1772-0.2409
213.4149-1.2572-0.66783.10511.55244.0557-0.0561-0.0172-0.1485-0.0297-0.15730.1765-0.1764-0.06350.16810.0535-0.02010.01440.05890.02320.05323.62873.8689-0.2516
222.0456-0.6677-0.63523.68091.02491.38120.0473-0.0997-0.26740.0419-0.0915-0.150.04820.01420.01910.06980.01-0.0260.10640.02950.14247.3437-0.79944.3753
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 121 through 132 )
2X-RAY DIFFRACTION2chain 'A' and (resid 133 through 146 )
3X-RAY DIFFRACTION3chain 'A' and (resid 147 through 162 )
4X-RAY DIFFRACTION4chain 'A' and (resid 163 through 195 )
5X-RAY DIFFRACTION5chain 'A' and (resid 196 through 204 )
6X-RAY DIFFRACTION6chain 'A' and (resid 205 through 221 )
7X-RAY DIFFRACTION7chain 'A' and (resid 222 through 231 )
8X-RAY DIFFRACTION8chain 'A' and (resid 232 through 256 )
9X-RAY DIFFRACTION9chain 'C' and (resid 124 through 132 )
10X-RAY DIFFRACTION10chain 'C' and (resid 133 through 146 )
11X-RAY DIFFRACTION11chain 'C' and (resid 147 through 168 )
12X-RAY DIFFRACTION12chain 'C' and (resid 169 through 195 )
13X-RAY DIFFRACTION13chain 'C' and (resid 196 through 204 )
14X-RAY DIFFRACTION14chain 'C' and (resid 205 through 211 )
15X-RAY DIFFRACTION15chain 'C' and (resid 212 through 255 )
16X-RAY DIFFRACTION16chain 'D' and (resid 121 through 132 )
17X-RAY DIFFRACTION17chain 'D' and (resid 133 through 146 )
18X-RAY DIFFRACTION18chain 'D' and (resid 147 through 168 )
19X-RAY DIFFRACTION19chain 'D' and (resid 169 through 195 )
20X-RAY DIFFRACTION20chain 'D' and (resid 196 through 209 )
21X-RAY DIFFRACTION21chain 'D' and (resid 210 through 221 )
22X-RAY DIFFRACTION22chain 'D' and (resid 222 through 256 )

+
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