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- PDB-2wft: Crystal structure of the human HIP ectodomain -

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Basic information

Entry
Database: PDB / ID: 2wft
TitleCrystal structure of the human HIP ectodomain
ComponentsHEDGEHOG-INTERACTING PROTEIN
KeywordsSIGNALING PROTEIN / MEMBRANE / SECRETED / CYTOPLASM / DEVELOPMENT / DISULFIDE BOND / EGF-LIKE DOMAIN / HEDGEHOG SIGNALLING / SIGNAL TRANSDUCTION / ALTERNATIVE SPLICING / POLYMORPHISM / GLYCOPROTEIN / CELL MEMBRANE
Function / homology
Function and homology information


regulation of fibroblast growth factor receptor signaling pathway / hedgehog family protein binding / Ligand-receptor interactions / dorsal/ventral pattern formation / skeletal system morphogenesis / ciliary membrane / epithelial tube branching involved in lung morphogenesis / neuroblast proliferation / negative regulation of signal transduction / negative regulation of smoothened signaling pathway ...regulation of fibroblast growth factor receptor signaling pathway / hedgehog family protein binding / Ligand-receptor interactions / dorsal/ventral pattern formation / skeletal system morphogenesis / ciliary membrane / epithelial tube branching involved in lung morphogenesis / neuroblast proliferation / negative regulation of signal transduction / negative regulation of smoothened signaling pathway / negative regulation of apoptotic process / cell surface / signal transduction / 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 / EGF-like domain, extracellular / EGF-like domain / Six-bladed beta-propeller, TolB-like / Laminin / Laminin ...Glucose/Sorbosone dehydrogenase / Glucose / Sorbosone dehydrogenase / Folate receptor-like / Folate receptor family / Soluble quinoprotein glucose/sorbosone dehydrogenase / 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 / Mainly Beta
Similarity search - Domain/homology
Hedgehog-interacting protein
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HEDGEHOG-INTERACTING PROTEIN
B: HEDGEHOG-INTERACTING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,4338
Polymers102,2582
Non-polymers1756
Water68538
1
A: HEDGEHOG-INTERACTING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,2104
Polymers51,1291
Non-polymers813
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: HEDGEHOG-INTERACTING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,2234
Polymers51,1291
Non-polymers943
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)100.976, 100.976, 305.916
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 215:274 OR RESSEQ 276:306 OR RESSEQ...
211CHAIN B AND (RESSEQ 215:274 OR RESSEQ 276:306 OR RESSEQ...

NCS oper: (Code: given
Matrix: (-0.6017, -0.7931, -0.09495), (-0.7875, 0.5692, 0.2363), (-0.1334, 0.217, -0.967)
Vector: 160.8, 44.49, 252.1)

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Components

#1: Protein HEDGEHOG-INTERACTING PROTEIN / HEDGEHOG-INTERACTING PROTEIN HIP / HIP / HHIP


Mass: 51129.043 Da / Num. of mol.: 2 / Fragment: C-TERMINAL DOMAIN, RESIDUES 214-671
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
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 4.88 Å3/Da / Density % sol: 74.6 % / Description: NONE
Crystal growDetails: 0.1 M TRIS-HCL, PH 8.5 3.5 M POTASSIUM FORMATE

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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: 2.8→20 Å / Num. obs: 45408 / % possible obs: 99.5 % / Observed criterion σ(I): 0 / Redundancy: 9.1 % / Biso Wilson estimate: 67.23 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 14.7
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 8.9 % / Rmerge(I) obs: 0.73 / Mean I/σ(I) obs: 3.4 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
HKL-2000data reduction
SCALEPACKdata scaling
autoSHARPphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.8→19.89 Å / SU ML: 0.32 / σ(F): 1.34 / Phase error: 23.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.238 2294 5.1 %
Rwork0.199 --
obs0.201 45390 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.64 Å2 / ksol: 0.32 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-6.2402 Å2-0 Å2-0 Å2
2--6.2402 Å20 Å2
3----12.4805 Å2
Refinement stepCycle: LAST / Resolution: 2.8→19.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6580 0 6 38 6624
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0146746
X-RAY DIFFRACTIONf_angle_d1.7249078
X-RAY DIFFRACTIONf_dihedral_angle_d19.8272484
X-RAY DIFFRACTIONf_chiral_restr0.117976
X-RAY DIFFRACTIONf_plane_restr0.0061194
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2875X-RAY DIFFRACTIONPOSITIONAL
12B2875X-RAY DIFFRACTIONPOSITIONAL0.131
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8001-2.86080.3521490.29742618X-RAY DIFFRACTION100
2.8608-2.92720.34041420.2812626X-RAY DIFFRACTION100
2.9272-3.00010.34561600.28042623X-RAY DIFFRACTION100
3.0001-3.0810.30011450.24552661X-RAY DIFFRACTION100
3.081-3.17130.29291460.23532685X-RAY DIFFRACTION100
3.1713-3.27320.23821500.2282631X-RAY DIFFRACTION100
3.2732-3.38960.25851340.21062681X-RAY DIFFRACTION100
3.3896-3.52460.26771500.19282656X-RAY DIFFRACTION100
3.5246-3.68410.23191330.18112669X-RAY DIFFRACTION100
3.6841-3.8770.20091410.1782728X-RAY DIFFRACTION100
3.877-4.11790.19111420.15882656X-RAY DIFFRACTION100
4.1179-4.43260.19521330.14092723X-RAY DIFFRACTION100
4.4326-4.87270.15731380.13292733X-RAY DIFFRACTION100
4.8727-5.56420.17231490.14422740X-RAY DIFFRACTION100
5.5642-6.96010.22031400.18252754X-RAY DIFFRACTION100
6.9601-19.8920.26841420.23572912X-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)
11.12781.17520.18981.62090.15722.7965-0.29060.20960.0733-0.7820.3814-0.0016-0.41110.15040.19430.6723-0.1250.06190.0680.01430.225982.391229.922296.0316
2-0.0069-0.3526-0.05970.02540.27470.8996-0.0597-0.2379-0.337-0.45510.02460.15840.2390.078400.5873-0.0033-0.05610.1217-0.04250.439176.952910.5907103.7939
3-0.28410.40870.61230.5208-0.47772.6735-0.0412-0.2057-0.0875-0.46460.0775-0.0429-0.30670.5959-00.4904-0.07320.11990.1964-0.04560.424586.955325.5032110.4514
40.02970.2795-0.48110.2094-0.11920.0342-0.339-0.57710.32960.05170.02380.23450.9486-1.4085-0.01880.6334-0.35330.11550.4590.0650.3051109.482461.862882.6065
50.96030.1190.19360.42770.07342.32850.168-0.3335-0.0054-0.0028-0.05250.0267-0.13210.0291-0.00010.1748-0.06520.06260.24750.00230.213472.654222.9081146.7886
60.9160.23780.80340.27040.50030.71140.0685-0.9809-0.22380.44760.1524-0.02710.04530.3987-0.00010.5456-0.1283-0.01620.9943-0.00230.376283.716819.6109162.6518
70.67560.1837-0.72930.4946-0.39882.95250.0909-0.4008-0.14650.1169-0.1113-0.07590.2010.38600.2718-0.0484-0.02220.34910.0570.398183.203715.9889140.886
80.34470.218-0.11110.1392-0.060.0842-0.27680.55330.1699-0.33560.06220.1111-1.17610.5627-0.00750.7676-0.21630.27290.5557-0.03810.51639.407413.275173.5493
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 214:484)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 485:532)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 533:624)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 625:671)
5X-RAY DIFFRACTION5(CHAIN B AND RESID 214:337)
6X-RAY DIFFRACTION6(CHAIN B AND RESID 338:490)
7X-RAY DIFFRACTION7(CHAIN B AND RESID 491:627)
8X-RAY DIFFRACTION8(CHAIN B AND RESID 628:670)

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