[English] 日本語
Yorodumi
- PDB-3d1m: Crystal Structure of Sonic Hedgehog Bound to the third FNIII doma... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3d1m
TitleCrystal Structure of Sonic Hedgehog Bound to the third FNIII domain of CDO
Components
  • Cell adhesion molecule
  • Sonic hedgehog protein
Keywordssignaling protein / cell adhesion / Fibronectin Protein-Protein Complex / Autocatalytic cleavage / Developmental protein / Glycoprotein / Hydrolase / Lipoprotein / Membrane / Palmitate / Protease / Secreted / Immunoglobulin domain / Transmembrane / signaling protein - cell adhesion COMPLEX
Function / homology
Function and homology information


forebrain regionalization / cell proliferation in external granule layer / epithelial-mesenchymal signaling involved in prostate gland development / Release of Hh-Np from the secreting cell / ventral spinal cord interneuron specification / skeletal muscle satellite cell differentiation / respiratory tube development / Ligand-receptor interactions / striated muscle tissue development / Activation of SMO ...forebrain regionalization / cell proliferation in external granule layer / epithelial-mesenchymal signaling involved in prostate gland development / Release of Hh-Np from the secreting cell / ventral spinal cord interneuron specification / skeletal muscle satellite cell differentiation / respiratory tube development / Ligand-receptor interactions / striated muscle tissue development / Activation of SMO / embryonic retina morphogenesis in camera-type eye / trachea development / positive regulation of skeletal muscle cell proliferation / right lung development / left lung development / primary prostatic bud elongation / regulation of mesenchymal cell proliferation involved in prostate gland development / mesenchymal smoothened signaling pathway involved in prostate gland development / positive regulation of sclerotome development / tracheoesophageal septum formation / negative regulation of ureter smooth muscle cell differentiation / positive regulation of ureter smooth muscle cell differentiation / negative regulation of kidney smooth muscle cell differentiation / positive regulation of kidney smooth muscle cell differentiation / regulation of odontogenesis / mesenchymal-epithelial cell signaling involved in prostate gland development / positive regulation of mesenchymal cell proliferation involved in ureter development / trunk neural crest cell migration / embryonic body morphogenesis / anatomical structure formation involved in morphogenesis / hindgut morphogenesis / polarity specification of anterior/posterior axis / negative regulation of alpha-beta T cell differentiation / regulation of prostatic bud formation / regulation of glial cell proliferation / formation of anatomical boundary / positive regulation of striated muscle cell differentiation / metanephric mesenchymal cell proliferation involved in metanephros development / regulation of epithelial cell proliferation involved in prostate gland development / trachea morphogenesis / cholesterol-protein transferase activity / telencephalon regionalization / bud outgrowth involved in lung branching / epithelial-mesenchymal cell signaling / Ligand-receptor interactions / laminin-1 binding / lung epithelium development / Hedgehog ligand biogenesis / vasculogenesis involved in coronary vascular morphogenesis / negative regulation of cholesterol efflux / salivary gland cavitation / myotube differentiation / spinal cord dorsal/ventral patterning / determination of left/right asymmetry in lateral mesoderm / negative regulation of mesenchymal cell apoptotic process / cell development / spinal cord motor neuron differentiation / positive regulation of cerebellar granule cell precursor proliferation / negative regulation of T cell differentiation in thymus / positive regulation of T cell differentiation in thymus / establishment of epithelial cell polarity / skeletal muscle cell proliferation / prostate gland development / intermediate filament organization / limb bud formation / stem cell development / embryonic skeletal system development / skeletal muscle fiber differentiation / cerebellar granule cell precursor proliferation / Activation of SMO / mesenchymal cell apoptotic process / patched binding / animal organ formation / embryonic digestive tract morphogenesis / lung lobe morphogenesis / hindbrain development / positive regulation of skeletal muscle tissue development / somite development / ectoderm development / embryonic foregut morphogenesis / epithelial cell proliferation involved in salivary gland morphogenesis / negative regulation of dopaminergic neuron differentiation / mesenchymal cell proliferation involved in lung development / neuron fate commitment / positive regulation of immature T cell proliferation in thymus / branching involved in prostate gland morphogenesis / mesenchymal cell proliferation / lymphoid progenitor cell differentiation / dorsal/ventral neural tube patterning / self proteolysis / smooth muscle tissue development / embryonic morphogenesis / artery development / positive regulation of astrocyte differentiation / CD4-positive or CD8-positive, alpha-beta T cell lineage commitment / negative thymic T cell selection / pattern specification process / regulation of stem cell proliferation / positive regulation of epithelial cell proliferation involved in prostate gland development / male genitalia development
Similarity search - Function
Muramoyl-pentapeptide Carboxypeptidase; domain 2 - #10 / Hedgehog, N-terminal signalling domain / Hedgehog protein / Hedgehog protein, Hint domain / : / Hint module / Hedgehog amino-terminal signalling domain / Muramoyl-pentapeptide Carboxypeptidase; domain 2 / Hedgehog signalling/DD-peptidase zinc-binding domain superfamily / Hint domain C-terminal ...Muramoyl-pentapeptide Carboxypeptidase; domain 2 - #10 / Hedgehog, N-terminal signalling domain / Hedgehog protein / Hedgehog protein, Hint domain / : / Hint module / Hedgehog amino-terminal signalling domain / Muramoyl-pentapeptide Carboxypeptidase; domain 2 / Hedgehog signalling/DD-peptidase zinc-binding domain superfamily / Hint domain C-terminal / Hint (Hedgehog/Intein) domain C-terminal region / Intein N-terminal splicing region / Intein N-terminal splicing motif profile. / Hint domain N-terminal / Hint (Hedgehog/Intein) domain N-terminal region / Hint domain superfamily / Immunoglobulin domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Fibronectin type III domain / Fibronectin type 3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Cell adhesion molecule-related/down-regulated by oncogenes / Sonic hedgehog protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å
AuthorsMcLellan, J.S. / Leahy, D.J.
CitationJournal: Nature / Year: 2008
Title: The mode of Hedgehog binding to Ihog homologues is not conserved across different phyla.
Authors: McLellan, J.S. / Zheng, X. / Hauk, G. / Ghirlando, R. / Beachy, P.A. / Leahy, D.J.
History
DepositionMay 6, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Sonic hedgehog protein
B: Sonic hedgehog protein
C: Cell adhesion molecule
D: Cell adhesion molecule
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,67410
Polymers61,3824
Non-polymers2916
Water7,386410
1
A: Sonic hedgehog protein
D: Cell adhesion molecule
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,8375
Polymers30,6912
Non-polymers1463
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Sonic hedgehog protein
C: Cell adhesion molecule
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,8375
Polymers30,6912
Non-polymers1463
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.179, 98.582, 144.047
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein Sonic hedgehog protein / SHH / HHG-1 / Sonic hedgehog protein N-product / Sonic hedgehog protein C-product


Mass: 19030.389 Da / Num. of mol.: 2
Fragment: N-terminal Domain, Sonic hedgehog protein N-product, residues 26-189
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Shh, Hhg1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q62226
#2: Protein Cell adhesion molecule


Mass: 11660.819 Da / Num. of mol.: 2 / Fragment: Fibronectin type-III domain 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDON, CDO / Production host: Escherichia coli (E. coli) / References: UniProt: Q4KMG0
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 410 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.06 Å3/Da / Density % sol: 40.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.3
Details: 28% PEG 3350, 200 mM MgCl2, 100 mM Tris pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.97893 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Aug 24, 2007
RadiationScattering type: x-ray
Radiation wavelengthWavelength: 0.97893 Å / Relative weight: 1
ReflectionResolution: 1.7→40 Å / Num. obs: 55705 / % possible obs: 99 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.086 / Χ2: 0.942 / Net I/σ(I): 10.3
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.471 / Num. unique all: 5054 / Χ2: 0.805 / % possible all: 91.1

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→30.56 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.941 / SU B: 4.545 / SU ML: 0.081 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.113 / ESU R Free: 0.114 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.229 2693 4.9 %RANDOM
Rwork0.186 ---
obs0.189 55421 99.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.158 Å2
Baniso -1Baniso -2Baniso -3
1--1.15 Å20 Å20 Å2
2---0.87 Å20 Å2
3---2.03 Å2
Refinement stepCycle: LAST / Resolution: 1.7→30.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3911 0 6 410 4327
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0214003
X-RAY DIFFRACTIONr_angle_refined_deg1.4161.9385412
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4285479
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.5924.369206
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.75915689
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3161524
X-RAY DIFFRACTIONr_chiral_restr0.1020.2563
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023094
X-RAY DIFFRACTIONr_nbd_refined0.2110.22014
X-RAY DIFFRACTIONr_nbtor_refined0.3060.22760
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1110.2362
X-RAY DIFFRACTIONr_metal_ion_refined0.0640.212
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.160.240
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1340.217
X-RAY DIFFRACTIONr_mcbond_it0.7991.52469
X-RAY DIFFRACTIONr_mcangle_it1.25123881
X-RAY DIFFRACTIONr_scbond_it2.03131773
X-RAY DIFFRACTIONr_scangle_it2.9854.51531
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 182 -
Rwork0.259 3455 -
all-3637 -
obs--89.36 %
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)
12.4525-0.33690.07641.8413-0.31310.7613-0.01730.2467-0.3038-0.08680.03580.06840.0540.1351-0.0185-0.1622-0.0212-0.0098-0.14-0.0179-0.135851.031-39.49418.529
21.63170.4235-0.19421.91060.06171.0982-0.00280.19640.1183-0.1412-0.0272-0.0423-0.1132-0.15130.03-0.1251-0.0073-0.0291-0.1110.0168-0.137448.59620.67416.238
32.2960.63520.05834.1223-0.36121.8607-0.08470.1753-0.2779-0.160.0077-0.73640.18970.01050.077-0.1523-0.01640.0527-0.1839-0.00630.014559.562-1.07919.163
42.6828-0.5269-0.04912.1534-0.38632.1044-0.05760.39270.2019-0.0220.09310.2157-0.1982-0.0918-0.0355-0.1213-0.0285-0.0394-0.12790.0785-0.072539.118-16.90217.165
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A41 - 188
2X-RAY DIFFRACTION2B40 - 189
3X-RAY DIFFRACTION3C829 - 924
4X-RAY DIFFRACTION4D826 - 924

+
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://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