PDB-4qpy: Crystal structure of C1QL2

ID or keywords:

Entry

Database: PDB / ID: 4qpy

Title

Crystal structure of C1QL2

Components

Complement C1q-like protein 2

Keywords

PROTEIN BINDING /

jelly roll fold / Brain-specific angiogenesis inhibitor adhesion G-protein coupled receptor 3 /

extracellular

Function / homology

Function and homology information

collagen trimer / protein-containing complex / extracellular region / identical protein binding
Similarity search - Function

Biological species

Mus musculus (house mouse)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.384 Å

Authors

Ressl, S. / Brunger, A.T.

Citation

Journal: 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

Deposition	Jun 25, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 15, 2015	Provider: repository / Type: Initial release
Revision 1.1	May 6, 2015	Group: Database references
Revision 1.2	Feb 28, 2024	Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4qpy.cif.gz	170.4 KB	Display	PDBx/mmCIF format
PDB format	pdb4qpy.ent.gz	141.8 KB	Display	PDB format
PDBx/mmJSON format	4qpy.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/qp/4qpy ftp://data.pdbj.org/pub/pdb/validation_reports/qp/4qpy	HTTPS FTP

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Related structure data

Related structure data	4qq2C 4qqhC 4qqlC 4qqoC 4qqpC C: citing same article (ref.)
Similar structure data	4qql-3 3tyj-1 4d7y-1 1o91-d 5wh8-d 2jg9-2 4qqh-1 2jg8-1 4yf6-1 3lu9-1 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Complement C1q-like protein 2

B: Complement C1q-like protein 2

C: Complement C1q-like protein 2

44.8 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	225.620, 225.620, 225.620
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	209
Space group name H-M	F432

#1: Protein	Complement C1q-like protein 2 / C1q and tumor necrosis factor-related protein 10 / C1q/TNF-related protein 10 / C1qTNF10 / CTRP10 Mass: 14936.505 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: C1ql2, C1qtnf10, Ctrp10 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q8CFR0
#2: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 112 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

Complement C1q-like protein 2 / C1q and tumor necrosis factor-related protein 10 / C1q/TNF-related protein 10 / C1qTNF10 / CTRP10

Mass: 14936.505 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Mus musculus (house mouse) / Gene: C1ql2, C1qtnf10, Ctrp10 / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q8CFR0

#2: Water

ChemComp-HOH / water /

Water

Mass: 18.015 Da / Num. of mol.: 112 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.67 Å³/Da / Density % sol: 53.93 %
Crystal grow	Temperature: 292.15 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 60% Tascimate, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 292.15K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9999 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 11, 2011
Radiation	Monochromator: Side scattering bent cube-root I-beam single crystal; asymmetric cut 4.965 degs Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9999 Å / Relative weight: 1
Reflection	Resolution: 2→56.405 Å / Num. obs: 20205 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3.7

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Processing

Software

Name	Version	Classification
Blu-Ice		data collection
PHASER		phasing
PHENIX	(phenix.refine: 1.8.2_1309)	refinement
MOSFLM		data reduction
SCALA		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.384→56.405 Å / SU ML: 0.28 / σ(F): 1.34 / Phase error: 21.81 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2159	1032	5.11 %	random
R_work	0.1695	-	-	-
all	0.1718	-	-	-
obs	0.1718	20200	99.98 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.384→56.405 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3090	0	0	112	3202

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	3172
X-RAY DIFFRACTION	f_angle_d	1.204	4293
X-RAY DIFFRACTION	f_dihedral_angle_d	13.909	1107
X-RAY DIFFRACTION	f_chiral_restr	0.082	440
X-RAY DIFFRACTION	f_plane_restr	0.005	563

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.3842-2.5099	0.2785	158	0.2518	2654	X-RAY DIFFRACTION	100
2.5099-2.6672	0.3118	136	0.2427	2673	X-RAY DIFFRACTION	100
2.6672-2.8731	0.2967	146	0.2254	2683	X-RAY DIFFRACTION	100
2.8731-3.1622	0.2433	144	0.1943	2710	X-RAY DIFFRACTION	100
3.1622-3.6197	0.196	146	0.1582	2715	X-RAY DIFFRACTION	100
3.6197-4.5601	0.1666	144	0.1313	2780	X-RAY DIFFRACTION	100
4.5601-56.4208	0.2134	158	0.1624	2953	X-RAY DIFFRACTION	100

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°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)
1	2.9237	-0.9191	-1.9481	4.1044	-2.4895	4.271	0.1173	0.7925	0.295	-0.9705	-0.2869	0.5524	0.6061	-0.6813	-0.271	0.3371	0.097	-0.0592	0.2891	0.0891	0.2919	-22.8933	22.3036	42.2691
2	2.0378	-3.209	-1.1907	4.6735	-2.8457	2.8352	-0.382	1.065	-2.3781	-1.8226	-0.1903	0.6643	2.4131	-0.0631	-0.6581	1.0676	-0.2025	-0.0576	0.5539	-0.1625	0.5541	-22.2086	7.768	40.0892
3	3.4997	-0.6104	0.7887	3.4711	0.8491	2.9969	-0.151	0.7344	-0.0296	-0.5427	0.457	-0.0415	0.0049	0.5948	-0.2347	0.4643	-0.0429	0.0764	0.3759	0.0198	0.2182	-17.6605	21.7873	40.2386
4	4.4782	1.2491	1.5332	6.6514	0.3627	3.3893	-0.3114	-0.052	0.3138	-0.639	0.0946	-0.0251	-0.1542	0.0455	-0.2465	0.2395	0.0322	0.043	0.1402	0.0065	0.128	-14.8214	21.4004	51.7462
5	3.0363	-1.5446	-0.3866	0.8866	-0.0243	4.7595	-0.2527	0.2712	-1.6898	-0.7339	0.2641	2.1525	0.8789	-0.3355	0.0481	0.4642	-0.0543	-0.1401	0.2844	-0.0111	0.8636	-31.834	3.9916	48.1502
6	9.4845	1.5311	-7.564	7.0971	-0.9678	5.5862	0.0221	0.3119	-0.4072	-0.1243	0.55	-0.5772	0.6721	0.3364	-0.2809	0.3587	0.0657	-0.0543	0.3006	-0.085	0.2914	-17.7494	9.2998	52.4379
7	2.1483	1.5177	-3.134	2.2683	-2.1744	4.6424	-0.4336	-0.6053	-1.4833	-0.8895	0.2572	3.4825	2.3773	-1.6642	-0.2967	1.1684	-0.3133	0.0462	0.575	0.21	1.8917	-38.8675	5.2709	50.6187
8	2.8099	0.3241	0.4642	3.3609	0.8425	4.6747	-0.1399	0.0967	-0.3733	-0.5308	0.1668	-0.3277	0.4979	0.5366	-0.2637	0.2999	0.0464	-0.0096	0.173	-0.0159	0.2125	-15.8586	15.6712	50.9378
9	2.1008	-1.0121	-4.1999	8.1916	5.1537	4.9411	0.7425	1.3645	-0.1395	-2.2891	0.3517	0.9476	0.0889	-0.6211	1.8708	0.6074	-0.2603	-0.2951	0.3472	0.0074	0.7103	-30.3259	10.1099	42.1019
10	5.0752	1.9178	-2.5553	4.0043	-0.9601	2.2363	-0.1173	0.9863	-0.0639	-0.468	0.3959	0.0078	0.1143	-0.0087	-0.045	0.3149	0.0584	0.0243	0.1767	0.0439	0.2605	-22.1273	23.3152	48.9249
11	1.7463	-3.4274	0.6486	6.6633	-1.158	9.0015	-0.5782	1.4677	0.4305	-0.7187	-0.8031	0.2485	-2.5825	0.1506	-0.3205	0.3456	-0.0139	-0.0293	0.495	-0.0409	0.6828	-9.891	32.2958	61.7899
12	3.2865	1.7016	-0.2123	7.6976	0.4832	1.7424	0.0909	-0.4977	-0.8221	0.3726	-0.1929	0.2375	0.6303	0.5406	-0.1893	0.4528	0.1447	0.024	0.2726	0.09	0.4975	-17.9204	11.2289	66.5239
13	9.5491	6.7888	-0.4489	4.9861	-0.144	1.5843	0.6619	-1.7485	-0.8929	2.7196	-0.6164	0.5391	0.9259	-1.3156	-0.0472	0.8903	0.0007	0.181	0.632	0.2325	0.4044	-26.4807	11.413	77.0447
14	1.4881	-0.2274	-0.496	0.9783	-0.629	2.4881	-0.6732	-0.5426	-0.1588	0.6158	-0.0045	-0.6391	0.1536	0.5486	0.1026	0.3915	0.1	-0.2436	0.3277	-0.0071	0.29	-14.0973	17.7271	70.817
15	4.7542	3.2716	-1.3691	3.4268	-0.0164	1.5969	0.0373	-0.4215	-0.039	0.4048	0.0175	-0.2372	0.1068	-0.1202	-0.2282	0.2209	0.0636	-0.0551	0.2351	0.0562	0.2302	-22.3487	23.4607	66.5734
16	2.8975	-0.9536	-1.5112	0.3678	0.1627	2.2618	-0.4864	-0.5131	-3.9656	0.6028	0.5868	1.157	2.3463	-1.461	-0.1573	0.9043	-0.2775	-0.0253	0.8887	0.0889	1.203	-37.87	4.1593	69.7829
17	7.1512	2.9867	1.0427	4.3454	1.8468	4.7107	0.2815	-0.5378	0.3031	1.0593	-0.3972	0.9985	0.0912	-0.4162	-0.173	0.5317	0.0713	0.1312	0.3634	0.0871	0.2573	-31.8777	20.2799	71.9529
18	8.432	1.718	-2.6604	3.8838	0.4896	1.1251	-1.2486	1.0682	-1.7435	0.4923	-0.0813	1.1313	1.7128	-1.0072	1.4945	1.704	-0.1977	-0.0179	1.6777	-0.0906	1.5017	-38.6565	2.8753	63.1404
19	5.9425	1.1359	-0.5224	0.4255	-1.1566	6.3477	-0.7061	-1.2964	-1.2924	0.081	0.7716	-0.5575	0.6845	-0.5674	-1.1273	0.3363	0.2115	0.058	-0.7853	0.6119	0.2555	-30.7816	14.1745	62.2973
20	2.4072	0.4378	0.1572	2.2085	0.3971	4.9392	-0.0289	-0.1569	-0.1747	0.8233	0.2549	0.0549	0.2353	0.072	-0.0788	0.292	0.1328	-0.0202	0.3265	0.012	0.174	-21.9399	19.6941	67.9164
21	0.2445	-0.0905	1.0129	5.7566	0.1971	6.3831	0.0615	-0.0912	0.0065	-0.2184	0.0954	0.766	-0.1996	-1.328	-0.3405	0.4357	0.161	0.0412	0.4237	0.0973	0.3364	-36.9506	32.5008	60.5888
22	6.022	2.7913	2.2073	7.9707	4.4789	8.7737	0.046	0.4324	0.5796	0.4979	0.1658	0.8083	-1.1042	-1.6338	0.2365	0.2193	0.1769	0.0928	0.622	0.1937	0.4403	-41.108	33.3979	59.4997
23	3.4632	-0.7368	0.8611	0.3324	0.4562	2.1885	-0.1177	-0.0118	0.6742	0.3372	0.4568	0.1655	-0.7323	-0.438	-0.2162	0.3334	0.1491	0.0907	0.2248	0.0687	0.379	-30.5938	36.9046	56.1141
24	6.0178	4.1487	4.371	6.4161	3.9526	7.7616	-0.5421	0.9731	-2.1313	-1.1652	-0.1397	1.2557	3.178	-2.9249	-0.4431	0.6565	-0.4196	0.0244	1.0766	-0.1048	1.0229	-46.7611	17.6759	55.7745
25	3.2438	3.673	3.2715	5.8968	6.0371	6.5337	0.7049	0.7038	-0.1501	0.2202	-0.0933	1.0398	1.3825	-0.8902	-0.8377	0.455	-0.1094	-0.2355	0.5603	0.2095	0.514	-42.8945	20.7106	49.1308
26	3.9677	1.2854	0.4295	2.0586	1.4589	1.091	-0.5114	0.6724	0.0336	-1.8581	0.1407	0.7062	-0.2741	-0.5538	-0.0092	0.4537	0.0129	-0.2246	0.3585	0.1325	0.3182	-35.9332	28.2357	45.7399
27	1.9809	-4.2957	-7.0362	1.765	2.8272	4.5888	-2.4371	-2.3715	-1.7848	0.0361	-0.2924	-0.6657	3.0306	-2.257	-1.2382	2.0622	-0.4651	-0.5399	1.3264	0.5299	1.025	-44.8275	11.4325	57.7383
28	4.7348	-0.0295	-0.1581	2.5746	1.2805	1.666	-0.1319	0.2136	0.4367	-0.472	0.3057	0.6095	-0.2272	-0.3262	-0.1103	0.3267	0.0613	-0.0702	0.3665	0.1353	0.3238	-33.6762	30.8302	49.914
29	5.0782	-0.2925	4.4612	2.1535	-0.6015	4.0301	-0.6588	-1.9573	-0.933	1.4832	0.2453	1.1107	-0.0413	-1.3152	0.1019	0.7655	0.1344	0.1726	0.7509	0.2157	0.8774	-43.9069	24.8685	65.3873
30	4.0436	1.503	-0.8432	7.8908	-0.5246	1.6935	-0.0093	0.0175	0.2457	0.0394	0.1912	0.2857	-0.2979	-0.2288	-0.1448	0.1752	0.0354	-0.0687	0.2468	-0.0019	0.1855	-28.0257	30.4683	58.3313

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 7:19)
2	X-RAY DIFFRACTION	2	(chain A and resid 20:26)
3	X-RAY DIFFRACTION	3	(chain A and resid 27:47)
4	X-RAY DIFFRACTION	4	(chain A and resid 48:58)
5	X-RAY DIFFRACTION	5	(chain A and resid 59:70)
6	X-RAY DIFFRACTION	6	(chain A and resid 71:85)
7	X-RAY DIFFRACTION	7	(chain A and resid 86:93)
8	X-RAY DIFFRACTION	8	(chain A and resid 94:112)
9	X-RAY DIFFRACTION	9	(chain A and resid 113:122)
10	X-RAY DIFFRACTION	10	(chain A and resid 123:137)
11	X-RAY DIFFRACTION	11	(chain B and resid 4:9)
12	X-RAY DIFFRACTION	12	(chain B and resid 10:19)
13	X-RAY DIFFRACTION	13	(chain B and resid 20:25)
14	X-RAY DIFFRACTION	14	(chain B and resid 26:47)
15	X-RAY DIFFRACTION	15	(chain B and resid 48:61)
16	X-RAY DIFFRACTION	16	(chain B and resid 62:68)
17	X-RAY DIFFRACTION	17	(chain B and resid 69:85)
18	X-RAY DIFFRACTION	18	(chain B and resid 86:91)
19	X-RAY DIFFRACTION	19	(chain B and resid 92:99)
20	X-RAY DIFFRACTION	20	(chain B and resid 100:137)
21	X-RAY DIFFRACTION	21	(chain C and resid 7:22)
22	X-RAY DIFFRACTION	22	(chain C and resid 23:30)
23	X-RAY DIFFRACTION	23	(chain C and resid 31:58)
24	X-RAY DIFFRACTION	24	(chain C and resid 59:67)
25	X-RAY DIFFRACTION	25	(chain C and resid 68:72)
26	X-RAY DIFFRACTION	26	(chain C and resid 73:85)
27	X-RAY DIFFRACTION	27	(chain C and resid 86:93)
28	X-RAY DIFFRACTION	28	(chain C and resid 94:115)
29	X-RAY DIFFRACTION	29	(chain C and resid 116:123)
30	X-RAY DIFFRACTION	30	(chain C and resid 124:137)

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