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- PDB-2wg3: Crystal structure of the complex between human hedgehog-interacti... -

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Basic information

Entry
Database: PDB / ID: 2wg3
TitleCrystal structure of the complex between human hedgehog-interacting protein HIP and desert hedgehog without calcium
Components
  • DESERT HEDGEHOG PROTEIN N-PRODUCT
  • HEDGEHOG-INTERACTING PROTEIN
KeywordsSIGNALING PROTEIN / LIPOPROTEIN / DEVELOPMENT / MEMBRANE / SECRETED / PROTEASE / PALMITATE / HYDROLASE / DEVELOPMENTAL PROTEIN / AUTOCATALYTIC CLEAVAGE / SIGNAL TRANSDUCTION / EGF-LIKE DOMAIN / DISEASE MUTATION / HEDGEHOG SIGNALING / GLYCOPROTEIN / CELL MEMBRANE / DISULFIDE BOND
Function / homology
Function and homology information


regulation of fibroblast growth factor receptor signaling pathway / hedgehog family protein binding / cholesterol-protein transferase activity / HHAT G278V doesn't palmitoylate Hh-Np / regulation of steroid biosynthetic process / Ligand-receptor interactions / Transcriptional regulation of testis differentiation / Activation of SMO / patched binding / Leydig cell differentiation ...regulation of fibroblast growth factor receptor signaling pathway / hedgehog family protein binding / cholesterol-protein transferase activity / HHAT G278V doesn't palmitoylate Hh-Np / regulation of steroid biosynthetic process / Ligand-receptor interactions / Transcriptional regulation of testis differentiation / Activation of SMO / patched binding / Leydig cell differentiation / self proteolysis / male sex determination / Release of Hh-Np from the secreting cell / positive regulation of smoothened signaling pathway / dorsal/ventral pattern formation / Class B/2 (Secretin family receptors) / skeletal system morphogenesis / cell fate specification / ciliary membrane / smoothened signaling pathway / epithelial tube branching involved in lung morphogenesis / spermatid development / protein autoprocessing / neuroblast proliferation / negative regulation of smoothened signaling pathway / negative regulation of signal transduction / myelination / Hedgehog ligand biogenesis / Hedgehog 'on' state / osteoblast differentiation / response to estrogen / response to estradiol / cell-cell signaling / peptidase activity / regulation of gene expression / Hydrolases; Acting on ester bonds / Golgi membrane / calcium ion binding / endoplasmic reticulum membrane / negative regulation of apoptotic process / cell surface / signal transduction / extracellular space / zinc ion binding / extracellular region / plasma membrane / cytoplasm
Similarity search - Function
Glucose/Sorbosone dehydrogenase / Glucose / Sorbosone dehydrogenase / Folate receptor-like / Folate receptor family / Soluble quinoprotein glucose/sorbosone dehydrogenase / Hedgehog, N-terminal signalling domain / Hedgehog protein / Hedgehog protein, Hint domain / Hint module / Hedgehog amino-terminal signalling domain ...Glucose/Sorbosone dehydrogenase / Glucose / Sorbosone dehydrogenase / Folate receptor-like / Folate receptor family / Soluble quinoprotein glucose/sorbosone dehydrogenase / 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 / 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 2. / EGF-like domain signature 1. / EGF-like domain / Ribbon / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Desert hedgehog protein / Hedgehog-interacting protein
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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_conn.ptnr2_label_seq_id / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DESERT HEDGEHOG PROTEIN N-PRODUCT
B: DESERT HEDGEHOG PROTEIN N-PRODUCT
C: HEDGEHOG-INTERACTING PROTEIN
D: HEDGEHOG-INTERACTING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,90316
Polymers140,9274
Non-polymers97612
Water2,216123
1
A: DESERT HEDGEHOG PROTEIN N-PRODUCT
C: HEDGEHOG-INTERACTING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,9528
Polymers70,4642
Non-polymers4886
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2860 Å2
ΔGint-67.47 kcal/mol
Surface area26320 Å2
MethodPISA
2
B: DESERT HEDGEHOG PROTEIN N-PRODUCT
D: HEDGEHOG-INTERACTING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,9528
Polymers70,4642
Non-polymers4886
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2500 Å2
ΔGint-61.75 kcal/mol
Surface area25600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.821, 110.701, 144.381
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11C
21D
12A
22B

NCS domain segments:

Refine code: 5

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ASNASNLYSLYSCC215 - 2522 - 39
211ASNASNLYSLYSDD215 - 2522 - 39
121LYSLYSTHRTHRCC262 - 30549 - 92
221LYSLYSTHRTHRDD262 - 30549 - 92
131HISHISCYSCYSCC317 - 435104 - 222
231HISHISCYSCYSDD317 - 435104 - 222
141PROPROGLNGLNCC490 - 523277 - 310
241PROPROGLNGLNDD490 - 523277 - 310
151TRPTRPGLUGLUCC530 - 630317 - 417
251TRPTRPGLUGLUDD530 - 630317 - 417
112ALAALALYSLYSAA39 - 881 - 50
212ALAALALYSLYSBB39 - 881 - 50
122ALAALASERSERAA95 - 19157 - 153
222ALAALASERSERBB95 - 19157 - 153

NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(-0.9984, -0.003371, 0.05601), (0.001286, -0.9993, -0.03721), (0.0561, -0.03708, 0.9977)-100.2, -0.3093, 21.69
2given(-0.9998, -0.000944, 0.01781), (0.000479, -0.9997, -0.02609), (0.01783, -0.02608, 0.9995)-0.9787, -0.0038, 0.1301

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Components

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Protein , 2 types, 4 molecules ABCD

#1: Protein DESERT HEDGEHOG PROTEIN N-PRODUCT / / DESERT HEDGEHOG PROTEIN / DHH / HHG-3


Mass: 18662.850 Da / Num. of mol.: 2
Fragment: N-TERMINAL SIGNALLING DOMAIN OF DHH, RESIDUES 40-194
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET22B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ROSETTA / References: UniProt: O43323
#2: Protein HEDGEHOG-INTERACTING PROTEIN / HHIP / HIP / HEDGEHOG-INTERACTING PROTEIN HIP


Mass: 51800.715 Da / Num. of mol.: 2 / 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

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Sugars , 1 types, 2 molecules

#6: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 133 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 123 / Source method: isolated from a natural source / Formula: H2O

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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: 3.27 Å3/Da / Density % sol: 62.07 % / Description: NONE
Crystal growDetails: 1.4 M SODIUM/POTASSIUM PHOSPHATE, PH 5.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9793
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.6→20 Å / Num. obs: 49775 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 10 % / Rmerge(I) obs: 0.18 / Net I/σ(I): 15.3
Reflection shellResolution: 2.6→2.7 Å / Redundancy: 10.1 % / Rmerge(I) obs: 0.81 / Mean I/σ(I) obs: 2.7 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0047refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 2WFQ AND 2WFT

2wfq

2wft


Resolution: 2.6→20 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.879 / SU B: 24.589 / SU ML: 0.236 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.499 / ESU R Free: 0.319 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.281 2592 5.1 %RANDOM
Rwork0.224 ---
obs0.227 48634 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.18 Å2
Baniso -1Baniso -2Baniso -3
1-8.65 Å20 Å20 Å2
2---3.41 Å20 Å2
3----5.23 Å2
Refinement stepCycle: LAST / Resolution: 2.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8811 0 46 123 8980
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0219063
X-RAY DIFFRACTIONr_bond_other_d0.0010.026298
X-RAY DIFFRACTIONr_angle_refined_deg1.3291.96712269
X-RAY DIFFRACTIONr_angle_other_deg0.8643.00415204
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.01951108
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.24223.372433
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.458151509
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1741575
X-RAY DIFFRACTIONr_chiral_restr0.0750.21316
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02110093
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021873
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3811.55545
X-RAY DIFFRACTIONr_mcbond_other0.0731.52279
X-RAY DIFFRACTIONr_mcangle_it0.73828922
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.18533518
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.9954.53347
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11C1959medium positional0.210.5
21A863medium positional0.150.5
12D2557loose positional0.435
22B1145loose positional0.45
11C1959medium thermal0.32
21A863medium thermal0.252
12D2557loose thermal0.3710
22B1145loose thermal0.3810
LS refinement shellResolution: 2.6→2.67 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.402 184 -
Rwork0.33 3477 -
obs--100 %
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)
11.98950.25730.31392.30560.31212.19540.0526-0.09160.00550.0284-0.06220.12560.0907-0.04690.00950.02970.00550.05030.1580.05440.1133-34.797-8.02720.827
23.35160.4055-0.00122.2268-0.83213.47810.0328-0.0418-0.1034-0.088-0.1081-0.2272-0.22640.18590.07540.1265-0.0345-0.07220.1079-0.01460.1138-66.1456.3653.932
31.68680.4437-0.08323.32230.13093.42970.08770.2020.05140.31160.08040.4214-0.4499-0.5652-0.1680.09990.07810.03360.1650.08290.1855-23.1819.737-15.778
42.0007-0.2443-0.47841.0716-0.26194.09710.0641-0.13670.04660.16710.0907-0.1946-0.04670.2168-0.15490.0670.04710.04490.14110.06170.2108-15.6053.248-1.547
52.04580.7187-0.26644.6203-0.05512.00260.05760.02480.04240.27240.0290.0365-0.3605-0.0534-0.08660.10520.0504-0.00530.22160.0470.0646-11.32313.675-15.483
62.32360.3006-0.09822.9591-0.14832.8274-0.07180.2252-0.0757-0.1290.1416-0.31720.03710.2623-0.06990.0075-0.00790.01170.1504-0.05750.0876-80.918-9.592-35.155
72.30620.61180.51340.84410.28532.55150.0132-0.09710.05010.07080.04980.0497-0.213-0.1299-0.06310.03840.0339-0.02290.1052-0.05230.1324-86.312-2.916-18.566
81.87830.4033-0.25293.0918-0.13761.5607-0.01040.0198-0.0170.14960.0166-0.0382-0.12860.0311-0.00610.0220.0252-0.00690.1971-0.02440.0923-91.461-13.758-31.632
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A39 - 198
2X-RAY DIFFRACTION2B39 - 192
3X-RAY DIFFRACTION3C215 - 318
4X-RAY DIFFRACTION4C319 - 479
5X-RAY DIFFRACTION5C480 - 639
6X-RAY DIFFRACTION6D215 - 318
7X-RAY DIFFRACTION7D319 - 479
8X-RAY DIFFRACTION8D480 - 638

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