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- PDB-5ybz: High resolution structure of complement C1q-like protein 3 C1q domain -

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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


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: 1.711 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

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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
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

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Components

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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

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Non-polymers , 6 types, 351 molecules

#2: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / 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 / Sulfate


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


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 / Water


Mass: 18.015 Da / Num. of mol.: 336 / 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: 2.1 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

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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

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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 )

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