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- PDB-3n1m: Crystal Structure of IhhN bound to BOCFn3 -

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Basic information

Entry
Database: PDB / ID: 3n1m
TitleCrystal Structure of IhhN bound to BOCFn3
Components
  • Brother of CDO
  • Indian hedgehog protein
KeywordsPROTEIN BINDING / Binding Sites / Cell Adhesion Molecules / Cell Cycle Proteins / Cell Line / Conserved Sequence / Fibronectins / Hedgehog Proteins / Immunoglobulin G / Membrane Glycoproteins / Membrane Proteins / Tertiary / Receptors / Cell Surface / Sequence Homology / Signal Transduction / Tumor Suppressor Proteins
Function / homology
Function and homology information


vitelline membrane formation / negative regulation of eye pigmentation / camera-type eye photoreceptor cell fate commitment / chondrocyte differentiation involved in endochondral bone morphogenesis / embryonic skeletal joint development / Formation of lateral plate mesoderm / negative regulation of alpha-beta T cell differentiation / embryonic camera-type eye morphogenesis / cholesterol-protein transferase activity / HHAT G278V doesn't palmitoylate Hh-Np ...vitelline membrane formation / negative regulation of eye pigmentation / camera-type eye photoreceptor cell fate commitment / chondrocyte differentiation involved in endochondral bone morphogenesis / embryonic skeletal joint development / Formation of lateral plate mesoderm / negative regulation of alpha-beta T cell differentiation / embryonic camera-type eye morphogenesis / cholesterol-protein transferase activity / HHAT G278V doesn't palmitoylate Hh-Np / RUNX2 regulates chondrocyte maturation / Ligand-receptor interactions / proteoglycan metabolic process / negative regulation of immature T cell proliferation in thymus / chondrocyte proliferation / embryonic digestive tract morphogenesis / negative regulation of T cell differentiation in thymus / positive regulation of T cell differentiation in thymus / retinal pigment epithelium development / epithelial cell-cell adhesion / Activation of SMO / patched binding / somite development / embryonic pattern specification / smooth muscle tissue development / epithelial cell morphogenesis / self proteolysis / head morphogenesis / Release of Hh-Np from the secreting cell / intein-mediated protein splicing / positive regulation of smoothened signaling pathway / pancreas development / negative regulation of chondrocyte differentiation / regulation of growth / Class B/2 (Secretin family receptors) / positive regulation of mesenchymal cell proliferation / positive regulation of alpha-beta T cell differentiation / cell fate specification / embryonic digit morphogenesis / smoothened signaling pathway / branching involved in blood vessel morphogenesis / Myogenesis / heart looping / protein autoprocessing / positive regulation of collagen biosynthetic process / neuron development / positive regulation of myoblast differentiation / maternal process involved in female pregnancy / bone resorption / response to mechanical stimulus / axonal growth cone / cell maturation / extracellular matrix / positive regulation of epithelial cell proliferation / axon guidance / skeletal system development / liver regeneration / Hedgehog ligand biogenesis / Hedgehog 'on' state / multicellular organism growth / cell-cell adhesion / osteoblast differentiation / cell-cell signaling / response to estradiol / peptidase activity / nervous system development / regulation of gene expression / in utero embryonic development / Hydrolases; Acting on ester bonds / Golgi membrane / axon / calcium ion binding / endoplasmic reticulum membrane / negative regulation of apoptotic process / positive regulation of transcription by RNA polymerase II / extracellular space / plasma membrane
Similarity search - Function
Unstructured linking region I-set and fnIII on Brother of CDO / Hedgehog, N-terminal signalling domain / Hedgehog protein / Hedgehog protein, Hint domain / : / Hint module / Hedgehog amino-terminal signalling domain / Muramoyl-pentapeptide Carboxypeptidase; domain 2 - #10 / Muramoyl-pentapeptide Carboxypeptidase; domain 2 / Hedgehog signalling/DD-peptidase zinc-binding domain superfamily ...Unstructured linking region I-set and fnIII on Brother of CDO / Hedgehog, N-terminal signalling domain / Hedgehog protein / Hedgehog protein, Hint domain / : / Hint module / Hedgehog amino-terminal signalling domain / Muramoyl-pentapeptide Carboxypeptidase; domain 2 - #10 / 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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Indian hedgehog protein / Brother of CDO
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.69 Å
AuthorsKavran, J.M. / Leahy, D.J.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: All mammalian Hedgehog proteins interact with cell adhesion molecule, down-regulated by oncogenes (CDO) and brother of CDO (BOC) in a conserved manner.
Authors: Kavran, J.M. / Ward, M.D. / Oladosu, O.O. / Mulepati, S. / Leahy, D.J.
History
DepositionMay 15, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 19, 2013Group: Database references
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_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_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_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_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
B: Indian hedgehog protein
C: Brother of CDO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,0045
Polymers31,8582
Non-polymers1463
Water6,575365
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.533, 62.533, 163.972
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Indian hedgehog protein / IHH / HHG-2 / Indian hedgehog protein N-product / Indian hedgehog protein C-product


Mass: 19122.406 Da / Num. of mol.: 1 / Fragment: N-terminal Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IHH / Production host: Escherichia coli (E. coli) / References: UniProt: Q14623
#2: Protein Brother of CDO / Protein BOC


Mass: 12736.038 Da / Num. of mol.: 1 / Fragment: Third FN3 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BOC, UNQ604/PRO1190 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9BWV1
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 365 / 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: 2.9 Å3/Da / Density % sol: 57.66 %
Crystal growTemperature: 298 K / Method: vapor diffusion
Details: 20% PEG3350, 200mM NaCl, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT
DetectorType: RIGAKU SATURN 944+ / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.69→25 Å / Num. obs: 41889 / Observed criterion σ(F): 1.23

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.69→24.86 Å / SU ML: 1.1 / σ(F): 0.04 / Phase error: 20.29 / Stereochemistry target values: ML
Details: Hydrogens were added to the model but not refined as suggested in the Phenix Refinement Program. Reference: Afonine, P.V., Grosse-Kunstleve, R.W. & Adams, P.D. (2005). CCP4 Newsl. 42, contribution 8.
RfactorNum. reflection% reflection
Rfree0.201 2002 5.11 %
Rwork0.1638 --
obs0.1657 39149 92.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 57.784 Å2 / ksol: 0.404 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.3526 Å20 Å2-0 Å2
2--1.3526 Å20 Å2
3----2.4367 Å2
Refinement stepCycle: LAST / Resolution: 1.69→24.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2103 0 3 365 2471
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0154150
X-RAY DIFFRACTIONf_angle_d1.1757459
X-RAY DIFFRACTIONf_dihedral_angle_d15.2581041
X-RAY DIFFRACTIONf_chiral_restr0.122301
X-RAY DIFFRACTIONf_plane_restr0.006648
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.69-1.73380.3239800.2621851X-RAY DIFFRACTION65
1.7338-1.78070.31781430.2382320X-RAY DIFFRACTION83
1.7807-1.83310.29111370.20542405X-RAY DIFFRACTION85
1.8331-1.89220.28331230.20162472X-RAY DIFFRACTION87
1.8922-1.95980.21691330.18032553X-RAY DIFFRACTION90
1.9598-2.03830.25311470.17362659X-RAY DIFFRACTION94
2.0383-2.1310.20581510.15992760X-RAY DIFFRACTION97
2.131-2.24330.21061480.15122780X-RAY DIFFRACTION97
2.2433-2.38370.20541580.14942795X-RAY DIFFRACTION98
2.3837-2.56760.1851620.14752799X-RAY DIFFRACTION98
2.5676-2.82560.21971710.15152839X-RAY DIFFRACTION99
2.8256-3.23380.19941570.15022865X-RAY DIFFRACTION99
3.2338-4.07130.15841510.13622935X-RAY DIFFRACTION100
4.0713-24.86320.16291410.16233114X-RAY DIFFRACTION99

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