[English] 日本語
Yorodumi
- PDB-3k7g: Crystal structure of the Indian Hedgehog N-terminal signalling domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3k7g
TitleCrystal structure of the Indian Hedgehog N-terminal signalling domain
ComponentsIndian hedgehog protein
KeywordsSIGNALING PROTEIN / alpha+beta sandwich / Autocatalytic cleavage / Cell membrane / Developmental protein / Disease mutation / Glycoprotein / Hydrolase / Lipoprotein / Membrane / Palmitate / Protease / Secreted
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 / 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 / embryonic digestive tract morphogenesis / somite development / smooth muscle tissue development / epithelial cell morphogenesis / self proteolysis / embryonic pattern specification / 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 alpha-beta T cell differentiation / cell fate specification / positive regulation of mesenchymal cell proliferation / embryonic digit morphogenesis / smoothened signaling pathway / branching involved in blood vessel morphogenesis / heart looping / protein autoprocessing / positive regulation of collagen biosynthetic process / maternal process involved in female pregnancy / neuron development / bone resorption / response to mechanical stimulus / cell maturation / extracellular matrix / positive regulation of epithelial cell proliferation / skeletal system development / liver regeneration / Hedgehog ligand biogenesis / Hedgehog 'on' state / multicellular organism growth / osteoblast differentiation / cell-cell signaling / response to estradiol / peptidase activity / regulation of gene expression / in utero embryonic development / Hydrolases; Acting on ester bonds / Golgi membrane / 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
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 ...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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Indian hedgehog protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsHe, Y.-X. / Kang, Y. / Zhang, W.J. / Yu, J. / Ma, G. / Zhou, C.-Z.
CitationJournal: To be Published
Title: Crystal structure of the Indian Hedgehog N-terminal signalling domain
Authors: He, Y.-X. / Kang, Y. / Zhang, W.J. / Yu, J. / Ma, G. / Zhou, C.-Z.
History
DepositionOct 13, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 26, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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 / _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.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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Indian hedgehog protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6577
Polymers21,1161
Non-polymers5426
Water4,468248
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)107.660, 53.350, 35.440
Angle α, β, γ (deg.)90.00, 91.32, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-247-

HOH

21B-282-

HOH

-
Components

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


Mass: 21115.633 Da / Num. of mol.: 1 / Fragment: Indian hedgehog protein N-product
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IHH / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosseta (DE3) / References: UniProt: Q14623
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 248 / 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: 2.41 Å3/Da / Density % sol: 48.95 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M Tris-HCl, pH 8.5, 2.0M (NH4)2SO4, VAPOR DIFFUSION, HANGING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 10, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.5→23.9 Å / Num. obs: 32115 / % possible obs: 99.7 % / Redundancy: 2.7 % / Biso Wilson estimate: 11.73 Å2 / Rmerge(I) obs: 0.03 / Net I/σ(I): 22.2
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.117 / Mean I/σ(I) obs: 10 / Num. unique all: 4650 / % possible all: 99.5

-
Processing

Software
NameVersionClassification
MAR345dtbdata collection
MOLREPphasing
PHENIX(phenix.refine)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1VHH

1vhh


Resolution: 1.5→21.311 Å / Occupancy max: 1 / Occupancy min: 0.56 / FOM work R set: 0.906 / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.41 / Phase error: 16.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1837 1627 5.07 %RANDOM
Rwork0.1721 30480 --
obs0.1727 32107 99.67 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.135 Å2 / ksol: 0.427 e/Å3
Displacement parametersBiso max: 47.89 Å2 / Biso mean: 13.648 Å2 / Biso min: 4.53 Å2
Baniso -1Baniso -2Baniso -3
1-1.628 Å20 Å20.441 Å2
2---0.044 Å2-0 Å2
3----1.584 Å2
Refinement stepCycle: LAST / Resolution: 1.5→21.311 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1260 0 27 248 1535
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051311
X-RAY DIFFRACTIONf_angle_d1.0731771
X-RAY DIFFRACTIONf_dihedral_angle_d16.711481
X-RAY DIFFRACTIONf_chiral_restr0.077181
X-RAY DIFFRACTIONf_plane_restr0.004229
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.54410.19591300.1762519X-RAY DIFFRACTION99
1.5441-1.5940.18511270.16632500X-RAY DIFFRACTION100
1.594-1.65090.17951480.16392525X-RAY DIFFRACTION100
1.6509-1.7170.2131390.17592543X-RAY DIFFRACTION100
1.717-1.79510.19151240.16492532X-RAY DIFFRACTION100
1.7951-1.88970.17421400.15372553X-RAY DIFFRACTION100
1.8897-2.0080.18291220.15172562X-RAY DIFFRACTION100
2.008-2.16290.15241410.1472530X-RAY DIFFRACTION100
2.1629-2.38030.16151160.15922575X-RAY DIFFRACTION100
2.3803-2.72410.19941400.1762548X-RAY DIFFRACTION100
2.7241-3.42980.18611400.16732547X-RAY DIFFRACTION100
3.4298-21.31260.1461600.15712546X-RAY DIFFRACTION98

+
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