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- PDB-2v9s: Second LRR domain of human Slit2 -

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Basic information

Entry
Database: PDB / ID: 2v9s
TitleSecond LRR domain of human Slit2
ComponentsSLIT HOMOLOG 2 PROTEIN N-PRODUCT
KeywordsSTRUCTURAL PROTEIN / DEVELOPMENTAL PROTEIN / NEUROGENESIS / DIFFERENTIATION / EGF-LIKE DOMAIN
Function / homology
Function and homology information


negative regulation of leukocyte chemotaxis / corticospinal neuron axon guidance through spinal cord / negative regulation of mononuclear cell migration / negative regulation of lamellipodium assembly / induction of negative chemotaxis / negative regulation of smooth muscle cell chemotaxis / negative regulation of retinal ganglion cell axon guidance / Roundabout binding / apoptotic process involved in luteolysis / negative regulation of monocyte chemotaxis ...negative regulation of leukocyte chemotaxis / corticospinal neuron axon guidance through spinal cord / negative regulation of mononuclear cell migration / negative regulation of lamellipodium assembly / induction of negative chemotaxis / negative regulation of smooth muscle cell chemotaxis / negative regulation of retinal ganglion cell axon guidance / Roundabout binding / apoptotic process involved in luteolysis / negative regulation of monocyte chemotaxis / chemorepulsion involved in postnatal olfactory bulb interneuron migration / negative regulation of cellular response to growth factor stimulus / cellular response to heparin / negative regulation of small GTPase mediated signal transduction / response to cortisol / negative regulation of chemokine-mediated signaling pathway / laminin-1 binding / axon extension involved in axon guidance / Netrin-1 signaling / Formation of the ureteric bud / GTPase inhibitor activity / Regulation of commissural axon pathfinding by SLIT and ROBO / Role of ABL in ROBO-SLIT signaling / negative regulation of smooth muscle cell migration / negative regulation of neutrophil chemotaxis / SLIT2:ROBO1 increases RHOA activity / Roundabout signaling pathway / Inactivation of CDC42 and RAC1 / negative regulation of actin filament polymerization / pulmonary valve morphogenesis / Signaling by ROBO receptors / negative regulation of vascular permeability / positive regulation of axonogenesis / motor neuron axon guidance / cell migration involved in sprouting angiogenesis / Activation of RAC1 / aortic valve morphogenesis / proteoglycan binding / negative regulation of endothelial cell migration / ureteric bud development / negative chemotaxis / retinal ganglion cell axon guidance / branching morphogenesis of an epithelial tube / ventricular septum morphogenesis / negative regulation of protein phosphorylation / cellular response to hormone stimulus / axon guidance / negative regulation of cell migration / negative regulation of cell growth / Regulation of expression of SLITs and ROBOs / heparin binding / positive regulation of apoptotic process / calcium ion binding / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / cytoplasm
Similarity search - Function
Leucine rich repeat C-terminal domain / Follistatin-like, N-terminal / Follistatin-N-terminal domain-like / : / Laminin G domain / EGF-like, conserved site / Human growth factor-like EGF / C-terminal cystine knot signature. / C-terminal cystine knot domain profile. / Laminin G domain profile. ...Leucine rich repeat C-terminal domain / Follistatin-like, N-terminal / Follistatin-N-terminal domain-like / : / Laminin G domain / EGF-like, conserved site / Human growth factor-like EGF / C-terminal cystine knot signature. / C-terminal cystine knot domain profile. / Laminin G domain profile. / Cystine knot, C-terminal / C-terminal cystine knot-like domain (CTCK) / Leucine rich repeat N-terminal domain / Laminin G domain / Laminin G domain / Leucine-rich repeat N-terminal domain / Leucine rich repeat N-terminal domain / Cysteine-rich flanking region, C-terminal / Leucine rich repeat C-terminal domain / Leucine Rich Repeat / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Leucine-rich repeat, SDS22-like subfamily / Alpha-Beta Horseshoe / EGF-like domain / EGF-type aspartate/asparagine hydroxylation site / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. / Aspartic acid and asparagine hydroxylation site. / EGF-like calcium-binding domain / Calcium-binding EGF-like domain / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Epidermal growth factor-like domain. / Leucine-rich repeat profile. / EGF-like domain profile. / EGF-like domain signature 1. / EGF-like domain signature 2. / EGF-like domain / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Concanavalin A-like lectin/glucanase domain superfamily / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Slit homolog 2 protein
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMorlot, C. / Cusack, S. / McCarthy, A.A.
Citation
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2007
Title: Production of Slit2 Lrr Domains in Mammalian Cells for Structural Studies and the Structure of Slit2 Domain 3
Authors: Morlot, C. / Hemrika, W. / Romijn, R.A. / Gros, P. / Cusack, S. / Mccarthy, A.A.
History
DepositionAug 25, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 25, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Refinement description / Version format compliance
Revision 1.2Nov 5, 2014Group: Atomic model / Derived calculations ...Atomic model / Derived calculations / Non-polymer description / Other / Structure summary
Revision 1.3Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_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: SLIT HOMOLOG 2 PROTEIN N-PRODUCT
B: SLIT HOMOLOG 2 PROTEIN N-PRODUCT
C: SLIT HOMOLOG 2 PROTEIN N-PRODUCT
D: SLIT HOMOLOG 2 PROTEIN N-PRODUCT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,0326
Polymers98,8344
Non-polymers1982
Water9,656536
1
A: SLIT HOMOLOG 2 PROTEIN N-PRODUCT


Theoretical massNumber of molelcules
Total (without water)24,7091
Polymers24,7091
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: SLIT HOMOLOG 2 PROTEIN N-PRODUCT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8012
Polymers24,7091
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: SLIT HOMOLOG 2 PROTEIN N-PRODUCT


Theoretical massNumber of molelcules
Total (without water)24,7091
Polymers24,7091
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: SLIT HOMOLOG 2 PROTEIN N-PRODUCT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8152
Polymers24,7091
Non-polymers1061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.360, 123.450, 127.650
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: HIS / Beg label comp-ID: HIS / End auth comp-ID: CYS / End label comp-ID: CYS / Refine code: 4 / Auth seq-ID: 272 - 478 / Label seq-ID: 4 - 210

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-1, 0.00206, 0.00065), (0.00205, 0.99998, -0.00568), (-0.00066, -0.00568, -0.99998)-60.36621, 0.10969, 24.11236
3given(0.96748, 0.22233, 0.12066), (0.23702, -0.96338, -0.12536), (0.08837, 0.14989, -0.98475)-6.70196, 15.84241, 30.33205
4given(-0.96887, 0.21699, -0.11922), (-0.23177, -0.96424, 0.12852), (-0.08707, 0.15215, 0.98451)-62.21901, -1.44533, 1.29202

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Components

#1: Protein
SLIT HOMOLOG 2 PROTEIN N-PRODUCT / SLIT-2 / SLIT2 / SLIT HOMOLOG 2 PROTEIN


Mass: 24708.551 Da / Num. of mol.: 4 / Fragment: SECOND LRR DOMAIN, RESIDUES 272-479
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): HEK293-EBNA1 / Production host: HOMO SAPIENS (human) / References: UniProt: O94813
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 536 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsSULFINIC CYSTEINE (CSD): OXIDIZED CYSTEINE

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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: 2.4 Å3/Da / Density % sol: 49 % / Description: NONE
Crystal growpH: 5.6
Details: 20-24% PEG 4000, 20% ISOPROPANOL, 0.1M NA CITRATE, PH=5.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.939
DetectorType: ADSC CCD / Detector: CCD / Date: May 8, 2006 / Details: TORODIAL MIRROR
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.939 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 61528 / % possible obs: 94.3 % / Observed criterion σ(I): 0 / Redundancy: 5.9 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 10.2
Reflection shellResolution: 2→2.1 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 4.6 / % possible all: 87.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→30 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.912 / SU B: 9.113 / SU ML: 0.132 / TLS residual ADP flag: UNVERIFIED / Cross valid method: THROUGHOUT / ESU R: 0.211 / ESU R Free: 0.186 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.261 3221 5.1 %RANDOM
Rwork0.213 ---
obs0.216 60317 97.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.28 Å2
Baniso -1Baniso -2Baniso -3
1--1.1 Å20 Å20 Å2
2--2.95 Å20 Å2
3----1.86 Å2
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6525 0 13 536 7074
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0226906
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6621.9859401
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.255890
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.46423.882304
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.156151297
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2351557
X-RAY DIFFRACTIONr_chiral_restr0.1140.21091
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025121
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2190.23126
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.310.24513
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1580.2505
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2930.270
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1820.226
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7771.54426
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.20226940
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.21332789
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.5014.52428
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 1476 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Amedium positional0.430.5
2Bmedium positional0.410.5
3Cmedium positional0.430.5
4Dmedium positional0.420.5
1Amedium thermal1.012
2Bmedium thermal1.012
3Cmedium thermal12
4Dmedium thermal1.032
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.288 227
Rwork0.264 4150
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)
11.27480.03590.01911.11830.00611.0828-0.0461-0.1736-0.0128-0.00360.00710.0583-0.0417-0.11930.039-0.064-0.0016-0.007-0.0136-0.0065-0.0573-44.2511-1.1294-3.3892
21.2265-0.10020.05651.2712-0.0490.9072-0.05420.08710.00760.00760.0173-0.0459-0.05370.10910.0369-0.06050.0034-0.0033-0.01740.0016-0.0638-16.117-1.026627.5727
31.0634-0.6025-0.00710.9921-0.16130.88620.0028-0.0053-0.0230.00180.00020.0694-0.0479-0.0463-0.003-0.049-0.0150.0035-0.0211-0.0079-0.0612-43.33482.944930.8776
41.28020.70170.06190.92640.1521.126-0.0047-0.0042-0.02420.00450.0229-0.0469-0.05140.1346-0.0182-0.03840.02550.0024-0.08270.0077-0.0524-17.05692.8859-6.7794
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A272 - 478
2X-RAY DIFFRACTION2B272 - 478
3X-RAY DIFFRACTION3C272 - 478
4X-RAY DIFFRACTION4D272 - 478

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