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- PDB-4qqh: Crystal structure of C1QL3 in space group H32 -

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Basic information

Entry
Database: PDB / ID: 4qqh
TitleCrystal structure of C1QL3 in space group H32
ComponentsComplement C1q-like protein 3
KeywordsPROTEIN BINDING / Jelly roll fold / C1q / Brain-specific angiogenesis inhibitor G-protein coupled receptor 3 / extracellular
Function / homology
Function and homology information


postsynaptic density assembly / collagen trimer / neurotransmitter receptor localization to postsynaptic specialization membrane / regulation of synapse organization / synaptic cleft / hippocampal mossy fiber to CA3 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 / 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: 1.2 Å
AuthorsRessl, S. / Brunger, A.T.
CitationJournal: Structure / Year: 2015
Title: Structures of C1q-like Proteins Reveal Unique Features among the C1q/TNF Superfamily.
Authors: Ressl, S. / Vu, B.K. / Vivona, S. / Martinelli, D.C. / Sudhof, T.C. / Brunger, A.T.
History
DepositionJun 27, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 15, 2015Provider: repository / Type: Initial release
Revision 1.1May 6, 2015Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Feb 28, 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 / struct_site
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_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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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_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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)15,9688
Polymers15,1811
Non-polymers7877
Water3,009167
1
A: Complement C1q-like protein 3
hetero molecules

A: Complement C1q-like protein 3
hetero molecules

A: Complement C1q-like protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,90324
Polymers45,5423
Non-polymers2,36121
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area7680 Å2
ΔGint-114 kcal/mol
Surface area12570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.230, 76.230, 125.407
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-203-

CD

21A-204-

CD

31A-205-

CD

41A-206-

CD

51A-337-

HOH

61A-360-

HOH

71A-438-

HOH

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Components

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


Mass: 15180.792 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: C1ql3, C1ql, Ctrp13 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9ESN4
#2: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cd
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 167 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.31 Å3/Da / Density % sol: 46.74 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 30% PEG400, 0.1 Na-acetate, 0.01M CdCl2, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 292.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 20, 2010
RadiationMonochromator: Liquid nitrogen-cooled double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.2→38.11 Å / Num. obs: 41170 / % possible obs: 93.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3.7

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Processing

Software
NameVersionClassification
Blu-IceIcedata collection
PHASERphasing
PHENIX(phenix.refine: 1.9_1692)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.2→31.921 Å / SU ML: 0.07 / σ(F): 1.34 / Phase error: 15.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1674 2067 5.02 %random
Rwork0.1538 ---
all0.1544 ---
obs0.1544 41168 93.48 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.2→31.921 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1017 0 7 167 1191
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071066
X-RAY DIFFRACTIONf_angle_d1.1361448
X-RAY DIFFRACTIONf_dihedral_angle_d12.991381
X-RAY DIFFRACTIONf_chiral_restr0.047150
X-RAY DIFFRACTIONf_plane_restr0.005190
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2-1.22790.19441120.17871588X-RAY DIFFRACTION58
1.2279-1.25860.20811100.16551990X-RAY DIFFRACTION72
1.2586-1.29270.16771150.15972357X-RAY DIFFRACTION84
1.2927-1.33070.17361370.16222484X-RAY DIFFRACTION91
1.3307-1.37370.17561220.1562711X-RAY DIFFRACTION97
1.3737-1.42280.1661680.15792729X-RAY DIFFRACTION100
1.4228-1.47970.15041140.15322820X-RAY DIFFRACTION100
1.4797-1.54710.14761290.14712787X-RAY DIFFRACTION100
1.5471-1.62860.15751650.14592763X-RAY DIFFRACTION100
1.6286-1.73070.14381610.13912748X-RAY DIFFRACTION100
1.7307-1.86430.14691380.14292788X-RAY DIFFRACTION100
1.8643-2.05180.15091600.13892789X-RAY DIFFRACTION100
2.0518-2.34870.15791590.14282799X-RAY DIFFRACTION100
2.3487-2.95880.19381450.15962836X-RAY DIFFRACTION100
2.9588-31.93250.18021320.16632912X-RAY DIFFRACTION98
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)
14.0346-0.79690.86393.0071-0.08332.85290.00890.39520.0429-0.28280.0814-0.0136-0.23810.0315-0.09550.0963-0.01110.01560.10980.0170.08534.47779.955517.3392
21.903-1.9705-3.31622.34433.85727.22510.1167-0.22730.3334-0.09640.284-0.3264-0.39030.5759-0.37790.1317-0.01710.00140.1168-0.02590.15145.700817.993935.7323
37.0694-2.9904-5.19632.2332.58954.65580.1631-0.25950.3146-0.13490.0908-0.2006-0.35410.2862-0.31850.1135-0.01270.00340.0902-0.00950.13892.933517.706330.5274
43.6398-0.66230.95121.2004-1.03841.44510.03210.28240.2932-0.0454-0.0693-0.0902-0.12120.06640.0220.124-0.00720.01740.10350.02790.12661.225217.391518.4369
50.8102-0.08210.36510.9336-0.16172.6165-0.0068-0.05080.05410.07570.0029-0.0128-0.1272-0.02130.01060.08070.0016-0.00110.0635-0.00460.0914-2.34449.877633.6484
60.908-0.42970.10381.6717-0.98461.63640.0153-0.0958-0.01030.08070.04930.0762-0.0542-0.0815-0.05390.07690.00550.010.0666-0.01740.0803-4.79838.504737.9977
70.68810.3939-0.34231.14670.07740.70470.02980.10670.1014-0.13080.01330.11650.0288-0.0636-0.05310.07760.0075-0.00880.09410.00460.0976-8.21529.303821.3967
81.3007-0.4231.5730.1551-0.50831.9369-0.1376-0.10320.17970.1016-0.0152-0.0002-0.4521-0.25940.20680.12350.0196-0.01820.0743-0.01240.1232-5.116916.105432.828
91.6918-0.9831-0.73371.1749-0.73322.8154-0.1018-0.09570.32790.112-0.0422-0.2303-0.22620.32950.08470.0745-0.0169-0.0110.07540.00670.12587.34410.290431.0505
105.22120.9561-0.06243.53141.4031.9718-0.03280.3851-0.1715-0.2296-0.0690.08060.1392-0.24750.09020.17330.0056-0.00050.1686-0.00980.0878-6.23035.115810.6978
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 8:12)
2X-RAY DIFFRACTION2(chain A and resid 13:21)
3X-RAY DIFFRACTION3(chain A and resid 22:31)
4X-RAY DIFFRACTION4(chain A and resid 32:49)
5X-RAY DIFFRACTION5(chain A and resid 50:74)
6X-RAY DIFFRACTION6(chain A and resid 75:94)
7X-RAY DIFFRACTION7(chain A and resid 95:107)
8X-RAY DIFFRACTION8(chain A and resid 108:117)
9X-RAY DIFFRACTION9(chain A and resid 118:132)
10X-RAY DIFFRACTION10(chain A and resid 133:137)

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