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- PDB-4dlo: Crystal structure of the GAIN and HormR domains of brain angiogen... -

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Basic information

Entry
Database: PDB / ID: 4dlo
TitleCrystal structure of the GAIN and HormR domains of brain angiogenesis inhibitor 3 (BAI3)
ComponentsBrain-specific angiogenesis inhibitor 3
KeywordsSIGNALING PROTEIN / GAIN domain / includes GPS motif / autoproteolytic fold / extracellular
Function / homology
Function and homology information


motor learning / maintenance of synapse structure / myoblast fusion / positive regulation of synapse assembly / neuron remodeling / regulation of dendrite morphogenesis / plasma membrane => GO:0005886 / synaptic cleft / negative regulation of angiogenesis / GTPase activator activity ...motor learning / maintenance of synapse structure / myoblast fusion / positive regulation of synapse assembly / neuron remodeling / regulation of dendrite morphogenesis / plasma membrane => GO:0005886 / synaptic cleft / negative regulation of angiogenesis / GTPase activator activity / G protein-coupled receptor activity / adenylate cyclase-activating G protein-coupled receptor signaling pathway / postsynapse / membrane => GO:0016020 / cell surface receptor signaling pathway / G protein-coupled receptor signaling pathway / plasma membrane
Similarity search - Function
Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #610 / Chondroitinase Ac; Chain A, domain 3 - #50 / GPCR, family 2, brain-specific angiogenesis inhibitor / GPCR, family 2, extracellular hormone receptor domain / GAIN domain, N-terminal / GPCR-Autoproteolysis INducing (GAIN) domain / Hormone receptor fold / Chondroitinase Ac; Chain A, domain 3 / GPCR proteolysis site, GPS, motif / GPS motif ...Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #610 / Chondroitinase Ac; Chain A, domain 3 - #50 / GPCR, family 2, brain-specific angiogenesis inhibitor / GPCR, family 2, extracellular hormone receptor domain / GAIN domain, N-terminal / GPCR-Autoproteolysis INducing (GAIN) domain / Hormone receptor fold / Chondroitinase Ac; Chain A, domain 3 / GPCR proteolysis site, GPS, motif / GPS motif / GAIN-B domain profile. / G-protein-coupled receptor proteolytic site domain / CUB domain / CUB domain profile. / Thrombospondin type 1 domain / Thrombospondin type-1 (TSP1) repeat superfamily / Thrombospondin type-1 (TSP1) repeat profile. / Thrombospondin type 1 repeats / Thrombospondin type-1 (TSP1) repeat / Hormone receptor domain / GPCR, family 2, extracellular hormone receptor domain / G-protein coupled receptors family 2 profile 1. / Domain present in hormone receptors / GPCR family 2, extracellular hormone receptor domain superfamily / G-protein coupled receptors family 2 signature 2. / GPCR, family 2, secretin-like, conserved site / GPCR, family 2, secretin-like / 7 transmembrane receptor (Secretin family) / GPCR, family 2-like / G-protein coupled receptors family 2 profile 2. / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Few Secondary Structures / Irregular / Alpha Horseshoe / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Adhesion G protein-coupled receptor B3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsArac, D. / Boucard, A.A. / Bolliger, M.F. / Nguyen, J. / Soltis, M. / Sudhof, T.C. / Brunger, A.T.
CitationJournal: Embo J. / Year: 2012
Title: A novel evolutionarily conserved domain of cell-adhesion GPCRs mediates autoproteolysis.
Authors: Arac, D. / Boucard, A.A. / Bolliger, M.F. / Nguyen, J. / Soltis, S.M. / Sudhof, T.C. / Brunger, A.T.
History
DepositionFeb 6, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 4, 2012Group: Database references
Revision 1.2Jul 16, 2014Group: Refinement description
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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_comp_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Brain-specific angiogenesis inhibitor 3
B: Brain-specific angiogenesis inhibitor 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,12615
Polymers86,5102
Non-polymers2,61613
Water2,990166
1
A: Brain-specific angiogenesis inhibitor 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7118
Polymers43,2551
Non-polymers1,4557
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Brain-specific angiogenesis inhibitor 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,4157
Polymers43,2551
Non-polymers1,1606
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)123.364, 128.008, 160.320
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Brain-specific angiogenesis inhibitor 3


Mass: 43255.230 Da / Num. of mol.: 2
Fragment: GAIN and HormR domains of BAI3, UNP residues 498-868
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BAI3, KIAA0550 / Plasmid: pACGP67a / Production host: Trichoplusia Ni (cabbage looper) / References: UniProt: O60242

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Sugars , 3 types, 4 molecules

#2: Polysaccharide beta-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta- ...beta-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpb1-3[DGlcpNAcb1-4]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1b_1-5]/1-2-1/a3-b1_a4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(3+1)][b-L-Fucp]{}[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#5: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 2 types, 175 molecules

#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 166 / 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: 2

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Sample preparation

CrystalDensity Matthews: 3.66 Å3/Da / Density % sol: 66.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 15% PEG6000, 0.1M sodium citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
1701
2701
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRL BL9-211
SYNCHROTRONSSRL BL9-221.6
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 7, 2009
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1double crystal monochromatorSINGLE WAVELENGTHMx-ray1
2double crystal monochromatorSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
111
21.61
ReflectionResolution: 2.3→44.4 Å / Num. all: 56590 / Num. obs: 56485 / % possible obs: 99.67 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shell
Resolution (Å)Diffraction-ID% possible all
2.3-2.381,2100
2.38-2.481,2100
2.48-2.591,2100
2.59-2.731,2100
2.73-2.91,2100
4.95-501,299.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHARPphasing
PHENIX(phenix.refine: 1.6.1_357)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.3→44.4 Å / SU ML: 0.3 / σ(F): 1.34 / Phase error: 21.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2281 2903 5.14 %random
Rwork0.186 ---
obs0.1882 56485 99.67 %-
all-56590 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 64.135 Å2 / ksol: 0.37 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.1237 Å20 Å2-0 Å2
2--4.9356 Å20 Å2
3----6.0593 Å2
Refinement stepCycle: LAST / Resolution: 2.3→44.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5417 0 172 166 5755
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095707
X-RAY DIFFRACTIONf_angle_d1.147724
X-RAY DIFFRACTIONf_dihedral_angle_d17.9862127
X-RAY DIFFRACTIONf_chiral_restr0.074904
X-RAY DIFFRACTIONf_plane_restr0.005960
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.33580.31751250.26052408X-RAY DIFFRACTION95
2.3358-2.37610.28511240.23692539X-RAY DIFFRACTION100
2.3761-2.41930.2711650.23222495X-RAY DIFFRACTION100
2.4193-2.46580.28191360.23332532X-RAY DIFFRACTION100
2.4658-2.51610.28521280.22112518X-RAY DIFFRACTION100
2.5161-2.57080.26821490.20382522X-RAY DIFFRACTION100
2.5708-2.63060.23031370.19582554X-RAY DIFFRACTION100
2.6306-2.69640.23871430.18872538X-RAY DIFFRACTION100
2.6964-2.76930.27171360.18842518X-RAY DIFFRACTION100
2.7693-2.85080.24221420.19122539X-RAY DIFFRACTION100
2.8508-2.94280.23811290.18042546X-RAY DIFFRACTION100
2.9428-3.04790.22121360.17572550X-RAY DIFFRACTION100
3.0479-3.16990.21131380.16572561X-RAY DIFFRACTION100
3.1699-3.31410.20331180.17092559X-RAY DIFFRACTION100
3.3141-3.48880.19571340.172560X-RAY DIFFRACTION100
3.4888-3.70730.19781500.16512568X-RAY DIFFRACTION100
3.7073-3.99340.22521440.16932567X-RAY DIFFRACTION100
3.9934-4.39490.20361290.16142584X-RAY DIFFRACTION100
4.3949-5.03010.19621480.14632588X-RAY DIFFRACTION100
5.0301-6.33450.21541470.18942621X-RAY DIFFRACTION100
6.3345-44.42220.23871450.19972715X-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)
10.2417-0.10390.10484.8877-1.13391.22590.01290.0526-0.10020.29720.23791.0919-0.2445-0.2418-0.28080.1848-0.01350.05070.30320.06850.4385-53.024523.10041.3773
23.6270.97780.17061.01240.25590.43290.39860.30340.24260.0975-0.2602-0.1392-0.07060.3914-0.11840.234-0.03110.04890.36260.04540.4059-41.256123.76075.4364
39.59844.4933.8284.73861.58172.13810.399-2.3275-0.43241.5572-0.8808-0.28460.0696-0.60030.10720.734-0.1621-0.1460.77210.13870.4586-17.091527.437822.7916
44.1893-0.22531.3020.12950.473.18410.39960.4402-1.0619-0.1539-0.19490.18751.0074-0.0135-0.11680.5487-0.023-0.00220.2662-0.06380.729-20.111519.84837.8851
53.29732.1095-0.78672.4656-0.89371.52850.2582-0.0997-0.05470.2259-0.20720.0347-0.0417-0.1102-0.01720.2114-0.09440.02940.279-0.02220.2898-18.816833.4229.5386
60.860.4004-0.47381.0961-0.63110.2817-0.03770.1317-0.1673-0.1915-0.1872-0.190.05740.13020.18160.2279-0.00520.0280.33850.00090.3208-3.179239.0451-2.9666
71.37780.209-0.84250.8713-0.88574.34330.0714-0.06880.30580.0603-0.09730.2126-0.5785-0.56120.00950.2090.04690.01470.27310.00330.3122-13.538747.7484-0.663
80.5010.19460.29831.0041-1.87572.6398-0.19170.07750.08420.03010.16210.2586-0.0485-0.82670.00830.1724-0.020.00820.4589-0.00970.2806-20.92746.9623-10.2622
91.71783.6129-0.28457.8519-1.94659.77740.50650.7551.142-0.4432-0.16832.1721-0.0612-0.8028-0.33690.45820.0407-0.11150.56250.11360.8944-21.694776.6955-79.4547
100.43130.9773-0.51311.4583-0.60781.34130.19010.008-0.08470.3052-0.1377-0.078-0.10490.0776-0.04420.2454-0.07390.00080.2776-0.01760.2919-13.604459.1171-65.9456
112.54440.40190.33722.6534-0.87840.5853-0.1060.2094-0.3268-0.69410.22010.13751.1478-0.6103-0.30970.479-0.3854-0.0940.45850.0010.2464-27.677944.6493-46.649
120.9630.23620.84280.25330.16725.2204-0.1894-0.0719-0.2841-0.00810.04970.0990.8159-0.69780.07490.4059-0.0950.01330.41990.06610.3149-22.352848.0676-42.1666
131.2612-0.47492.37871.9155-1.2729.8574-0.5212-0.208-0.05430.42610.2042-0.0869-1.0771-1.20920.22390.39170.0637-0.0640.45350.02280.243-22.887354.9443-33.1928
144.0021-0.56382.54682.428-3.51746.3899-1.1743-0.92310.34941.22850.362-0.2645-3.0221-0.18750.70211.31570.2383-0.25810.4523-0.11280.3286-18.73664.0151-18.3488
150.43-0.58791.33480.6196-2.01466.2427-1.13490.49070.67040.57650.3409-0.258-2.9279-0.18160.83441.5639-0.1081-0.34060.41340.07160.4385-17.840368.6609-35.1951
161.7173-0.65111.34350.2225-0.33434.9045-0.9490.10080.98611.0053-0.095-0.6899-3.36510.25830.95652.4944-0.0526-0.67460.23730.05410.8087-16.86776.6891-31.1689
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 508:527 )A508 - 527
2X-RAY DIFFRACTION2( CHAIN A AND RESID 528:572 )A528 - 572
3X-RAY DIFFRACTION3( CHAIN A AND RESID 573:601 )A573 - 601
4X-RAY DIFFRACTION4( CHAIN A AND RESID 602:611 )A602 - 611
5X-RAY DIFFRACTION5( CHAIN A AND RESID 612:690 )A612 - 690
6X-RAY DIFFRACTION6( CHAIN A AND RESID 691:740 )A691 - 740
7X-RAY DIFFRACTION7( CHAIN A AND RESID 741:803 )A741 - 803
8X-RAY DIFFRACTION8( CHAIN A AND RESID 804:866 )A804 - 866
9X-RAY DIFFRACTION9( CHAIN B AND RESID 501:509 )B501 - 509
10X-RAY DIFFRACTION10( CHAIN B AND RESID 510:563 )B510 - 563
11X-RAY DIFFRACTION11( CHAIN B AND RESID 564:595 )B564 - 595
12X-RAY DIFFRACTION12( CHAIN B AND RESID 596:627 )B596 - 627
13X-RAY DIFFRACTION13( CHAIN B AND RESID 628:702 )B628 - 702
14X-RAY DIFFRACTION14( CHAIN B AND RESID 703:765 )B703 - 765
15X-RAY DIFFRACTION15( CHAIN B AND RESID 766:796 )B766 - 796
16X-RAY DIFFRACTION16( CHAIN B AND RESID 801:864 )B801 - 864

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