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

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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 / hindgut morphogenesis / polarity specification of anterior/posterior axis / anatomical structure formation involved in morphogenesis / 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 / vasculogenesis involved in coronary vascular morphogenesis / laminin-1 binding / Hedgehog ligand biogenesis / lung epithelium development / salivary gland cavitation / negative regulation of cholesterol efflux / spinal cord dorsal/ventral patterning / negative regulation of mesenchymal cell apoptotic process / determination of left/right asymmetry in lateral mesoderm / myotube differentiation / cell development / spinal cord motor neuron differentiation / negative regulation of T cell differentiation in thymus / establishment of epithelial cell polarity / positive regulation of T cell differentiation in thymus / skeletal muscle cell proliferation / prostate gland development / intermediate filament organization / limb bud formation / embryonic skeletal system development / stem cell development / skeletal muscle fiber differentiation / positive regulation of cerebellar granule cell precursor proliferation / animal organ formation / mesenchymal cell apoptotic process / patched binding / embryonic digestive tract morphogenesis / hindbrain development / somite development / positive regulation of skeletal muscle tissue 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 / mesenchymal cell proliferation / positive regulation of immature T cell proliferation in thymus / lung lobe morphogenesis / self proteolysis / smooth muscle tissue development / dorsal/ventral neural tube patterning / branching involved in prostate gland morphogenesis / artery development / lymphoid progenitor cell differentiation / embryonic morphogenesis / positive regulation of astrocyte differentiation / CD4-positive or CD8-positive, alpha-beta T cell lineage commitment / regulation of stem cell proliferation / positive regulation of epithelial cell proliferation involved in prostate gland development / negative thymic T cell selection / pattern specification process / 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

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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)68,5939
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

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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

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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: 3.14 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

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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

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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: 3.2→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)

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