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- PDB-4nn0: Crystal structure of the C1QTNF5 globular domain in space group P63 -

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Basic information

Entry
Database: PDB / ID: 4nn0
TitleCrystal structure of the C1QTNF5 globular domain in space group P63
ComponentsComplement C1q tumor necrosis factor-related protein 5
KeywordsCELL ADHESION / L-ORMD / late onset retinal macular degeneration / S163R / 10-strand jelly-roll fold / Cellular adhesion
Function / homology
Function and homology information


collagen trimer / inner ear development / protein secretion / lateral plasma membrane / bicellular tight junction / transport vesicle / cell projection / apical plasma membrane / extracellular space / identical protein binding / plasma membrane
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
ACETATE ION / Complement C1q tumor necrosis factor-related protein 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.42 Å
AuthorsTu, X. / Palczewski, K.
CitationJournal: J.Struct.Biol. / Year: 2014
Title: The macular degeneration-linked C1QTNF5 (S163) mutation causes higher-order structural rearrangements.
Authors: Tu, X. / Palczewski, K.
History
DepositionNov 15, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 26, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 23, 2014Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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 tumor necrosis factor-related protein 5
B: Complement C1q tumor necrosis factor-related protein 5
C: Complement C1q tumor necrosis factor-related protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,79626
Polymers49,2733
Non-polymers1,52423
Water5,296294
1
A: Complement C1q tumor necrosis factor-related protein 5
hetero molecules

A: Complement C1q tumor necrosis factor-related protein 5
hetero molecules

A: Complement C1q tumor necrosis factor-related protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,97345
Polymers49,2733
Non-polymers2,70042
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 area12630 Å2
ΔGint-3 kcal/mol
Surface area15660 Å2
MethodPISA
2
B: Complement C1q tumor necrosis factor-related protein 5
hetero molecules

B: Complement C1q tumor necrosis factor-related protein 5
hetero molecules

B: Complement C1q tumor necrosis factor-related protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,95727
Polymers49,2733
Non-polymers1,68524
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area9780 Å2
ΔGint-42 kcal/mol
Surface area16280 Å2
MethodPISA
3
C: Complement C1q tumor necrosis factor-related protein 5
hetero molecules

C: Complement C1q tumor necrosis factor-related protein 5
hetero molecules

C: Complement C1q tumor necrosis factor-related protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,4596
Polymers49,2733
Non-polymers1863
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 area7830 Å2
ΔGint-8 kcal/mol
Surface area15600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.603, 50.603, 268.531
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11A-313-

SO4

21A-313-

SO4

31B-306-

SO4

41B-306-

SO4

51A-401-

HOH

61A-429-

HOH

71A-510-

HOH

81A-514-

HOH

91A-518-

HOH

101B-401-

HOH

111B-427-

HOH

121B-503-

HOH

131B-509-

HOH

141C-401-

HOH

Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.496073, 0.868275, -0.003155), (0.868273, 0.496081, 0.002471), (0.00371, -0.001514, -0.999992)-25.2918, 14.73086, -11.95059

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Components

#1: Protein Complement C1q tumor necrosis factor-related protein 5


Mass: 16424.301 Da / Num. of mol.: 3 / Fragment: globular domain (UNP residues 103-243)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: C1QTNF5, CTRP5, UNQ303/PRO344 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9BXJ0
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 294 / 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: 2.01 Å3/Da / Density % sol: 38.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 2 M ammonium sulfate, 0.1 M sodium acetate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS / Detector: PIXEL / Date: Jul 11, 2012
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.42→134.27 Å / Num. all: 72461 / Num. obs: 72440 / % possible obs: 99.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 3 / Redundancy: 8.2 % / Rmerge(I) obs: 0.041 / Net I/σ(I): 30.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allDiffraction-ID% possible all
1.42-1.53.90.1228.410017193.8
4.49-134.278.90.036562368199.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.7.0029refinement
DPSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4F3J

4f3j


Resolution: 1.42→134.265 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.972 / SU B: 1.173 / SU ML: 0.022 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.01 / ESU R Free: 0.01 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.14168 3645 5 %RANDOM
Rwork0.10438 ---
obs0.10622 68699 99.03 %-
all-72440 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 26.409 Å2
Baniso -1Baniso -2Baniso -3
1-7.05 Å20 Å20 Å2
2--7.05 Å20 Å2
3----14.1 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.14 Å0.14 Å
Luzzati d res low-5 Å
Luzzati sigma a0.07 Å0.07 Å
Refinement stepCycle: LAST / Resolution: 1.42→134.265 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3241 0 95 294 3630
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0193476
X-RAY DIFFRACTIONr_bond_other_d0.0030.023162
X-RAY DIFFRACTIONr_angle_refined_deg1.6451.9444707
X-RAY DIFFRACTIONr_angle_other_deg1.38437269
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5735425
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.02223.077156
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.49815480
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.561518
X-RAY DIFFRACTIONr_chiral_restr0.1040.2486
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213960
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02860
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr19.7736638
X-RAY DIFFRACTIONr_sphericity_free38.543551
X-RAY DIFFRACTIONr_sphericity_bonded24.35656796
LS refinement shellResolution: 1.42→1.456 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.147 223 -
Rwork0.097 4530 -
obs--87.95 %

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