[English] 日本語
Yorodumi
- PDB-2wfx: Crystal structure of the complex between human hedgehog-interacti... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2wfx
TitleCrystal structure of the complex between human hedgehog-interacting protein HIP and Sonic Hedgehog in the presence of calcium
Components
  • HEDGEHOG-INTERACTING PROTEIN
  • SONIC HEDGEHOG PROTEIN N-PRODUCT
KeywordsSIGNALING PROTEIN / AUTOCATALYTIC CLEAVAGE / PROTEASE / MEMBRANE / SECRETED / PALMITATE / HYDROLASE / SIGNAL TRANSDUCTION / DEVELOPMENTAL PROTEIN / LIPOPROTEIN / DEVELOPMENT / GLYCOPROTEIN / CELL MEMBRANE / DISULFIDE BOND / EGF-LIKE DOMAIN / HEDGEHOG SIGNALING
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 / respiratory tube development / Ligand-receptor interactions / striated muscle tissue development / regulation of fibroblast growth factor receptor signaling pathway / 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 / respiratory tube development / Ligand-receptor interactions / striated muscle tissue development / regulation of fibroblast growth factor receptor signaling pathway / Activation of SMO / 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 / 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 / formation of anatomical boundary / positive regulation of striated muscle cell differentiation / regulation of glial cell proliferation / metanephric mesenchymal cell proliferation involved in metanephros development / regulation of epithelial cell proliferation involved in prostate gland development / trachea morphogenesis / hedgehog family protein binding / cholesterol-protein transferase activity / telencephalon regionalization / bud outgrowth involved in lung branching / epithelial-mesenchymal cell signaling / Ligand-receptor interactions / lung epithelium development / Hedgehog ligand biogenesis / vasculogenesis involved in coronary vascular morphogenesis / laminin-1 binding / salivary gland cavitation / negative regulation of cholesterol efflux / myotube differentiation / spinal cord dorsal/ventral patterning / negative regulation of mesenchymal cell apoptotic process / determination of left/right asymmetry in lateral mesoderm / cell development / spinal cord motor neuron differentiation / 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 / positive regulation of cerebellar granule cell precursor proliferation / mesenchymal cell apoptotic process / patched binding / animal organ formation / hindbrain development / embryonic digestive tract morphogenesis / 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 / cerebellar granule cell precursor proliferation / 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 / lung lobe morphogenesis / 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 / branching involved in salivary gland morphogenesis / epithelial cell proliferation involved in prostate gland development
Similarity search - Function
Glucose/Sorbosone dehydrogenase / Glucose / Sorbosone dehydrogenase / Folate receptor-like / Folate receptor family / Muramoyl-pentapeptide Carboxypeptidase; domain 2 - #10 / Hedgehog, N-terminal signalling domain / Hedgehog protein / Hedgehog protein, Hint domain / : / Hint module ...Glucose/Sorbosone dehydrogenase / Glucose / Sorbosone dehydrogenase / Folate receptor-like / Folate receptor family / Muramoyl-pentapeptide Carboxypeptidase; domain 2 - #10 / Hedgehog, N-terminal signalling domain / Hedgehog protein / Hedgehog protein, Hint domain / : / Hint module / Hedgehog amino-terminal signalling domain / Soluble quinoprotein glucose/sorbosone dehydrogenase / 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 / EGF-like domain, extracellular / EGF-like domain / Six-bladed beta-propeller, TolB-like / Laminin / Laminin / Epidermal growth factor-like domain. / EGF-like domain profile. / EGF-like domain signature 1. / EGF-like domain signature 2. / EGF-like domain / Ribbon / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Sonic hedgehog protein / Hedgehog-interacting protein
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
HOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsBishop, B. / Aricescu, A.R. / Harlos, K. / O'Callaghan, C.A. / Jones, E.Y. / Siebold, C.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2009
Title: Structural Insights Into Hedgehog Ligand Sequestration by the Human Hedgehog-Interacting Protein Hip
Authors: Bishop, B. / Aricescu, A.R. / Harlos, K. / O'Callaghan, C.A. / Jones, E.Y. / Siebold, C.
History
DepositionApr 15, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 30, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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_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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: SONIC HEDGEHOG PROTEIN N-PRODUCT
B: HEDGEHOG-INTERACTING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,5939
Polymers68,3382
Non-polymers2557
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2360 Å2
ΔGint-90.88 kcal/mol
Surface area26460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.150, 89.150, 171.429
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

-
Components

#1: Protein SONIC HEDGEHOG PROTEIN N-PRODUCT / SONIC HEDGEHOG SHH / SONIC HEDGEHOG PROTEIN / HHG-1 / SHH


Mass: 17366.393 Da / Num. of mol.: 1
Fragment: N-TERMINAL SIGNALLING DOMAIN OF SHH, RESIDUES 40-191
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Description: IMAGE CLONE / Plasmid: PHLSEC
Cell line (production host): HUMAN EMBRYONIC KIDNEY (HEK) 293T CELLS
Production host: HOMO SAPIENS (human) / References: UniProt: Q62226
#2: Protein HEDGEHOG-INTERACTING PROTEIN / HHIP / HIP / HEDGEHOG-INTERACTING PROTEIN HIP


Mass: 50971.848 Da / Num. of mol.: 1 / Fragment: C-TERMINAL DOMAIN OF HIP, RESIDUES 214-670
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Description: IMAGE CLONE / Plasmid: PHLSEC
Cell line (production host): HUMAN EMBRYONIC KIDNEY (HEK) 293T CELLS
Production host: HOMO SAPIENS (human) / References: UniProt: Q96QV1
#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.: 3 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.14 Å3/Da / Density % sol: 67 % / Description: NONE
Crystal growDetails: 0.1 M SODIUM ACETATE, PH 4.6 0.5 M POTASSIUM THIOCYANATE 5 MM CACL

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9792
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.2→20 Å / Num. obs: 13529 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Biso Wilson estimate: 60.28 Å2 / Rmerge(I) obs: 0.19 / Net I/σ(I): 10.6
Reflection shellResolution: 3.2→3.3 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.73 / Mean I/σ(I) obs: 2.5 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1VHH AND 2WFT

1vhh

2wft


Resolution: 3.2→19.774 Å / SU ML: 0.48 / σ(F): 1.33 / Phase error: 32.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3003 1056 7.9 %
Rwork0.24 --
obs0.2448 13372 99.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 7.909 Å2 / ksol: 0.248 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-12.8101 Å20 Å2-0 Å2
2--12.8101 Å20 Å2
3----25.6202 Å2
Refinement stepCycle: LAST / Resolution: 3.2→19.774 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4465 0 7 0 4472
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044592
X-RAY DIFFRACTIONf_angle_d0.5246166
X-RAY DIFFRACTIONf_dihedral_angle_d13.4331680
X-RAY DIFFRACTIONf_chiral_restr0.032667
X-RAY DIFFRACTIONf_plane_restr0.002810
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2001-3.34510.38531320.32721519X-RAY DIFFRACTION100
3.3451-3.52050.37271380.28561508X-RAY DIFFRACTION100
3.5205-3.73970.38341350.30121448X-RAY DIFFRACTION95
3.7397-4.02620.34121180.24181509X-RAY DIFFRACTION98
4.0262-4.42720.21671090.18141575X-RAY DIFFRACTION100
4.4272-5.05850.22541280.16071547X-RAY DIFFRACTION100
5.0585-6.33810.24061450.19691576X-RAY DIFFRACTION100
6.3381-19.77390.30531510.26741634X-RAY DIFFRACTION100
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)
1-2.4294-3.13344.7324.91351.61742.1742-0.0499-0.821-1.23160.46651.4941-0.7643-0.0026-0.2846-1.14990.5297-0.1245-0.11631.037-0.21380.6838-15.535322.8480.345
23.1371-1.8838-0.49537.57431.6011-4.91820.54951.09680.1377-1.5653-0.4481-0.230.0118-0.2764-0.06820.86070.0941-0.00321.0365-0.01060.4562-11.83334.0435-19.9891
31.3094-0.4983-0.70011.44620.53892.65020.22471.1195-0.1708-0.3408-0.15390.4019-0.1673-1.1965-0.14070.51650.0075-0.08860.97480.03040.597-26.329536.9906-9.4577
41.14350.24771.28330.0843-0.58121.3815-0.20390.20140.10940.00430.33890.00460.1828-0.705-0.17830.29920.0356-0.07030.7566-0.17850.4464-16.992432.7139-5.8563
51.5604-0.7924-0.18740.12350.48410.4431-0.01970.49950.3204-0.0475-0.0054-0.1371-0.09530.4436-0.01380.3652-0.0163-0.0330.7194-0.05060.527720.156545.091917.4177
6-0.0457-0.37370.42481.3461-0.30781.1187-0.04910.2367-0.1060.0121-0.07610.03420.0209-0.09270.09060.27230.0659-0.02130.7624-0.09810.39373.001834.619812.687
70.79050.72180.38971.2980.01431.0919-0.0249-0.54640.25770.1862-0.08510.31930.0958-0.38450.01530.15970.1170.0120.7029-0.10890.4017-2.188744.973530.0318
81.2024-0.1183-0.13881.2333-0.0028-0.03510.2409-0.28810.1975-0.1675-0.1381-0.54380.04830.0114-0.10520.27320.12150.02170.7627-0.05590.3617.266335.220122.3916
98.3785-0.2192.63733.5831-0.93091.82690.30350.16571.041-1.0186-0.927-0.14150.6768-0.1210.52891.66440.5014-0.25141.5525-0.19461.23515.4861-1.5974-6.2923
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 40:50)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 51:77)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 78:129)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 130:188)
5X-RAY DIFFRACTION5(CHAIN B AND RESID 215:276)
6X-RAY DIFFRACTION6(CHAIN B AND RESID 277:442)
7X-RAY DIFFRACTION7(CHAIN B AND RESID 443:530)
8X-RAY DIFFRACTION8(CHAIN B AND RESID 531:637)
9X-RAY DIFFRACTION9(CHAIN B AND RESID 638:666)

+
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