[English] 日本語
Yorodumi
- PDB-2v9s: Second LRR domain of human Slit2 -

+
Open data


ID or keywords:

Loading...

-
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 lamellipodium assembly / induction of negative chemotaxis / negative regulation of mononuclear cell migration / negative regulation of retinal ganglion cell axon guidance / apoptotic process involved in luteolysis / negative regulation of monocyte chemotaxis / chemorepulsion involved in postnatal olfactory bulb interneuron migration / Roundabout binding ...negative regulation of leukocyte chemotaxis / corticospinal neuron axon guidance through spinal cord / negative regulation of lamellipodium assembly / induction of negative chemotaxis / negative regulation of mononuclear cell migration / negative regulation of retinal ganglion cell axon guidance / apoptotic process involved in luteolysis / negative regulation of monocyte chemotaxis / chemorepulsion involved in postnatal olfactory bulb interneuron migration / Roundabout binding / negative regulation of smooth muscle cell chemotaxis / negative regulation of cellular response to growth factor stimulus / cellular response to heparin / negative regulation of small GTPase mediated signal transduction / negative regulation of chemokine-mediated signaling pathway / response to cortisol / laminin-1 binding / negative regulation of smooth muscle cell migration / axon extension involved in axon guidance / Formation of the ureteric bud / Netrin-1 signaling / GTPase inhibitor activity / Role of ABL in ROBO-SLIT signaling / Regulation of commissural axon pathfinding by SLIT and ROBO / negative regulation of neutrophil chemotaxis / SLIT2:ROBO1 increases RHOA activity / Roundabout signaling pathway / Inactivation of CDC42 and RAC1 / negative regulation of actin filament polymerization / Signaling by ROBO receptors / pulmonary valve morphogenesis / negative regulation of vascular permeability / aortic valve morphogenesis / cell migration involved in sprouting angiogenesis / Activation of RAC1 / motor neuron axon guidance / proteoglycan binding / negative regulation of endothelial cell migration / ureteric bud development / negative chemotaxis / positive regulation of axonogenesis / retinal ganglion cell axon guidance / branching morphogenesis of an epithelial tube / ventricular septum morphogenesis / cellular response to hormone stimulus / negative regulation of cell migration / negative regulation of protein phosphorylation / axon guidance / 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. / Leucine rich repeat N-terminal domain / Cystine knot, C-terminal ...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. / Leucine rich repeat N-terminal domain / Cystine knot, C-terminal / C-terminal cystine knot-like domain (CTCK) / Laminin G domain profile. / Leucine-rich repeat N-terminal domain / Leucine rich repeat N-terminal domain / Laminin G domain / Laminin G domain / Leucine Rich Repeat / Cysteine-rich flanking region, C-terminal / Leucine rich repeat C-terminal domain / 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 2. / Leucine-rich repeat / EGF-like domain signature 1. / EGF-like domain / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A272 - 478
2114B272 - 478
3114C272 - 478
4114D272 - 478

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

-
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
Nonpolymer detailsSULFINIC CYSTEINE (CSD): OXIDIZED CYSTEINE

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more