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- PDB-2wg4: Crystal structure of the complex between human hedgehog-interacti... -

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Basic information

Entry
Database: PDB / ID: 2wg4
TitleCrystal structure of the complex between human hedgehog-interacting protein HIP and sonic hedgehog without 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 / regulation of glial cell proliferation / negative regulation of alpha-beta T cell differentiation / regulation of prostatic bud formation / 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 / hedgehog family protein binding / cholesterol-protein transferase activity / myotube differentiation / telencephalon regionalization / bud outgrowth involved in lung branching / epithelial-mesenchymal cell signaling / Ligand-receptor interactions / Hedgehog ligand biogenesis / laminin-1 binding / lung epithelium development / vasculogenesis involved in coronary vascular morphogenesis / negative regulation of cholesterol efflux / salivary gland cavitation / spinal cord dorsal/ventral patterning / determination of left/right asymmetry in lateral mesoderm / negative regulation of mesenchymal cell apoptotic process / positive regulation of cerebellar granule cell precursor proliferation / negative regulation of T cell differentiation in thymus / cell development / spinal cord motor neuron differentiation / positive regulation of T cell differentiation in thymus / establishment of epithelial cell polarity / intermediate filament organization / prostate gland development / cerebellar granule cell precursor proliferation / limb bud formation / embryonic skeletal system development / skeletal muscle fiber differentiation / lung lobe morphogenesis / mesenchymal cell apoptotic process / patched binding / animal organ formation / embryonic digestive tract morphogenesis / embryonic foregut morphogenesis / hindbrain development / positive regulation of skeletal muscle tissue development / epithelial cell proliferation involved in salivary gland morphogenesis / somite development / ectoderm development / neuron fate commitment / negative regulation of dopaminergic neuron differentiation / mesenchymal cell proliferation involved in lung development / skeletal muscle cell proliferation / stem cell development / 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 / embryonic morphogenesis / self proteolysis / smooth muscle tissue development / artery development / thalamus 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 / oligodendrocyte development / positive regulation of epithelial cell proliferation involved in prostate gland development / male genitalia 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: 3.15 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 1.3Nov 8, 2017Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.host_org_common_name / _entity_src_gen.pdbx_host_org_scientific_name
Revision 1.4Dec 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.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 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)68,7377
Polymers68,5802
Non-polymers1575
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2180 Å2
ΔGint-75.73 kcal/mol
Surface area26650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.055, 88.055, 171.946
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 SONIC HEDGEHOG PROTEIN N-PRODUCT / SONIC HEDGEHOG SHH / SONIC HEDGEHOG PROTEIN / HHG-1 / SHH


Mass: 17607.682 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) / 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) / 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-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
Has protein modificationY

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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: 3.08 Å3/Da / Density % sol: 67 % / Description: NONE
Crystal growDetails: 0.1 M SODIUM ACETATE, PH 4.6 0.5 M POTASSIUM THIOCYANATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.89
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.89 Å / Relative weight: 1
ReflectionResolution: 3.15→20 Å / Num. obs: 13878 / % possible obs: 99.2 % / Observed criterion σ(I): 0 / Redundancy: 7.5 % / Biso Wilson estimate: 58.58 Å2 / Rmerge(I) obs: 0.21 / Net I/σ(I): 9.9
Reflection shellResolution: 3.15→3.25 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.88 / Mean I/σ(I) obs: 2.8 / % possible all: 99.8

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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: 3.15→19.842 Å / SU ML: 0.5 / σ(F): 1.9 / Phase error: 26.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.292 678 4.9 %
Rwork0.2335 --
obs0.2364 13824 53.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 25.941 Å2 / ksol: 0.317 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.1237 Å20 Å2-0 Å2
2--3.1237 Å20 Å2
3----6.2475 Å2
Refinement stepCycle: LAST / Resolution: 3.15→19.842 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4455 0 5 0 4460
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024571
X-RAY DIFFRACTIONf_angle_d0.4976151
X-RAY DIFFRACTIONf_dihedral_angle_d13.8251679
X-RAY DIFFRACTIONf_chiral_restr0.035662
X-RAY DIFFRACTIONf_plane_restr0.002805
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1501-3.39220.34131440.28852559X-RAY DIFFRACTION53
3.3922-3.73160.32551490.24692559X-RAY DIFFRACTION53
3.7316-4.26690.26211240.21182623X-RAY DIFFRACTION53
4.2669-5.35820.25561370.18672638X-RAY DIFFRACTION54
5.3582-19.84260.29621240.25922767X-RAY DIFFRACTION56
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)
15.7571.65843.01214.9871-1.87526.71050.4391-0.74270.66810.3481-0.7234-0.9425-0.290.38680.17590.5249-0.06040.01490.62790.16550.603516.1113-21.47450.3391
21.1092-0.75450.14064.59070.9588-0.12450.15270.3709-0.0955-1.2523-0.113-0.2085-0.3475-0.1446-0.04340.8003-0.01920.03280.86440.17780.489211.3948-32.5908-19.9011
3-2.695-1.2965-0.56432.52460.83722.10960.15320.7545-0.0703-0.0577-0.0232-1.11180.40450.8629-0.06790.4072-0.00370.0971.07870.11861.06227.2349-34.5573-9.9634
42.5788-1.2856-0.7183.8241.25062.3506-0.3452-0.1642-0.4456-0.18980.0536-0.66320.14680.51070.36020.4786-0.04170.04480.7240.17450.580117.3017-31.4994-6.0051
51.7346-0.6479-0.22242.3923-1.68220.78360.13810.038-0.58-0.1059-0.0030.44040.246-0.4005-0.15290.4562-0.0448-0.0060.70030.10230.5949-19.8267-44.370117.0235
63.14060.2272-0.21331.9325-0.69042.235-0.1428-0.06120.07710.08180.0125-0.0818-0.06620.24370.10250.4034-0.0047-0.03760.59470.09830.4227-2.5251-33.763712.5131
72.06580.0839-0.5072-0.2398-0.79071.29130.1104-0.6509-0.00150.06210.00460.2030.0910.2721-0.10130.44650.0337-0.05960.84680.13650.55772.0938-44.617629.9903
81.933-0.08560.63062.1701-1.53680.62810.1042-0.4678-0.2025-0.14170.16620.5404-0.0684-0.3142-0.20970.5698-0.03110.01850.72070.05970.5062-16.8388-34.376922.3161
97.2019-6.9671-1.40083.1623-1.64763.03281.1144-1.4527-0.6254-3.0351-0.4691.74270.06420.7669-0.53321.04570.1409-0.03520.5114-0.05230.9893-13.9444.1008-6.2016
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)

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