[English] 日本語
Yorodumi
- PDB-3n1o: Crystal structure of IhhN -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3n1o
TitleCrystal structure of IhhN
ComponentsIndian hedgehog protein
KeywordsPROTEIN BINDING / Binding Sites / Calcium / 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 / RUNX2 regulates chondrocyte maturation ...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 / RUNX2 regulates chondrocyte maturation / HHAT G278V doesn't palmitoylate Hh-Np / Ligand-receptor interactions / chondrocyte proliferation / negative regulation of immature T cell proliferation in thymus / negative regulation of T cell differentiation in thymus / positive regulation of T cell differentiation in thymus / epithelial cell-cell adhesion / retinal pigment epithelium development / proteoglycan metabolic process / Activation of SMO / patched binding / embryonic digestive tract morphogenesis / somite development / epithelial cell morphogenesis / self proteolysis / smooth muscle tissue development / Release of Hh-Np from the secreting cell / embryonic pattern specification / head morphogenesis / intein-mediated protein splicing / positive regulation of smoothened signaling pathway / pancreas development / Class B/2 (Secretin family receptors) / regulation of growth / negative regulation of chondrocyte differentiation / 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 / neuron development / bone resorption / maternal process involved in female pregnancy / response to mechanical stimulus / cell maturation / extracellular matrix / positive regulation of epithelial cell proliferation / liver regeneration / skeletal system development / 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
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 / 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: 2.55 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 16, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 26, 2023Group: Database references / Derived calculations
Category: citation / database_2 ...citation / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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_asym_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Indian hedgehog protein
B: Indian hedgehog protein
C: Indian hedgehog protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,6047
Polymers57,3673
Non-polymers2364
Water2,144119
1
A: Indian hedgehog protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,1882
Polymers19,1221
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Indian hedgehog protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,1882
Polymers19,1221
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Indian hedgehog protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2283
Polymers19,1221
Non-polymers1052
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.965, 67.965, 243.281
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11B-214-

HOH

-
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.: 3 / 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: Chemical ChemComp-ZN / ZINC ION


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


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / 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: 2.45 Å3/Da / Density % sol: 49.77 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6
Details: 1M NaCitrate, 100mM Cacodylate, pH 6.0, VAPOR DIFFUSION, temperature 298K

-
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: 2.55→50 Å / Num. obs: 18164

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.55→30.99 Å / SU ML: 0.92 / σ(F): 1.35 / Phase error: 24.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2605 935 5.15 %
Rwork0.1962 --
obs0.1995 18151 92.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.339 Å2 / ksol: 0.418 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.5584 Å20 Å20 Å2
2---1.5584 Å2-0 Å2
3---3.1167 Å2
Refinement stepCycle: LAST / Resolution: 2.55→30.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3630 0 4 119 3753
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043711
X-RAY DIFFRACTIONf_angle_d0.8515011
X-RAY DIFFRACTIONf_dihedral_angle_d18.0431374
X-RAY DIFFRACTIONf_chiral_restr0.057523
X-RAY DIFFRACTIONf_plane_restr0.003657
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.55-2.68310.34131310.22642498X-RAY DIFFRACTION96
2.6831-2.85110.32161310.22372523X-RAY DIFFRACTION97
2.8511-3.07110.25171350.22252496X-RAY DIFFRACTION96
3.0711-3.37980.29661440.1882404X-RAY DIFFRACTION92
3.3798-3.86810.22981460.16812318X-RAY DIFFRACTION89
3.8681-4.87030.20351250.15092347X-RAY DIFFRACTION87
4.8703-30.99270.25621230.21012630X-RAY DIFFRACTION92
Refinement TLS params.Method: refined / Origin x: 5.5508 Å / Origin y: -29.1867 Å / Origin z: 41.9078 Å
111213212223313233
T0.0721 Å2-0.0027 Å20.0034 Å2-0.0889 Å20.0152 Å2--0.0903 Å2
L0.1827 °2-0.0023 °2-0.0659 °2-0.0496 °2-0.0542 °2--0.4617 °2
S0.0079 Å °0.0029 Å °0.0174 Å °0.0266 Å °-0.0043 Å °0.0269 Å °0.0621 Å °0.0179 Å °-0 Å °
Refinement TLS groupSelection details: all

+
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