[English] 日本語
Yorodumi
- PDB-7pgm: HHIP-C in complex with heparin -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7pgm
TitleHHIP-C in complex with heparin
ComponentsHedgehog-interacting protein
KeywordsSIGNALING PROTEIN / HHIP / Hedgehog / morphogen / signalling / glycosaminoglycan / cholesterol / palmitate / secreted
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 / cell surface / signal transduction / extracellular region / zinc ion binding / 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 / Epidermal growth factor-like domain. / EGF-like domain profile. ...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 / Epidermal growth factor-like domain. / EGF-like domain profile. / EGF-like domain signature 1. / EGF-like domain signature 2. / EGF-like domain
Similarity search - Domain/homology
Hedgehog-interacting protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsGriffiths, S.C. / Schwab, R.A. / El Omari, K. / Bishop, B. / Iverson, E.J. / Malinuskas, T. / Dubey, R. / Qian, M. / Covey, D.F. / Gilbert, R.J.C. ...Griffiths, S.C. / Schwab, R.A. / El Omari, K. / Bishop, B. / Iverson, E.J. / Malinuskas, T. / Dubey, R. / Qian, M. / Covey, D.F. / Gilbert, R.J.C. / Rohatgi, R. / Siebold, C.
Funding support United Kingdom, United States, 7items
OrganizationGrant numberCountry
Cancer Research UKC20724/A14414 United Kingdom
Cancer Research UKC20724/A26752 United Kingdom
European Research Council (ERC)647278 United Kingdom
National Institutes of Health/National Cancer Institute (NIH/NCI)HL067773 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)GM118082 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)GM106078 United States
Wellcome Trust099675/Z/12/Z United Kingdom
CitationJournal: Nat Commun / Year: 2021
Title: Hedgehog-Interacting Protein is a multimodal antagonist of Hedgehog signalling.
Authors: Griffiths, S.C. / Schwab, R.A. / El Omari, K. / Bishop, B. / Iverson, E.J. / Malinauskas, T. / Dubey, R. / Qian, M. / Covey, D.F. / Gilbert, R.J.C. / Rohatgi, R. / Siebold, C.
History
DepositionAug 14, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 15, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 22, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Hedgehog-interacting protein
B: Hedgehog-interacting protein
C: Hedgehog-interacting protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,8414
Polymers157,5143
Non-polymers2,3281
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation, Large clusters of HHIP-C are observed to be assembled in the presence of heparin via sedimentation velocity analytical ultracentrifugation experiments
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6130 Å2
ΔGint17 kcal/mol
Surface area62520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)170.637, 105.252, 148.433
Angle α, β, γ (deg.)90.00, 95.97, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Hedgehog-interacting protein / HHIP / HIP


Mass: 52504.500 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: HHIP-C, the C-terminal domain of HHIP, recombinantly expressed in and purified from HEK293T cells using the pHLsec vector for mammalian secretion
Source: (gene. exp.) Homo sapiens (human) / Gene: HHIP, HIP, UNQ5825/PRO19644 / Plasmid: pHLsec / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: Q96QV1
#2: Polysaccharide 2-O-sulfo-alpha-L-idopyranuronic acid-(1-3)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose- ...2-O-sulfo-alpha-L-idopyranuronic acid-(1-3)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 2327.897 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/2,8,7/[a2122h-1a_1-5_2*NSO/3=O/3=O_6*OSO/3=O/3=O][a2121A-1a_1-5_2*OSO/3=O/3=O]/1-2-1-2-1-2-1-2/a4-b1_b4-c1_c4-d1_d4-e1_e4-f1_f4-g1_g3-h1WURCSPDB2Glycan 1.1.0
[][a-D-GlcpNSO36SO3]{[(4+1)][a-L-IdopA2SO3]{[(4+1)][a-D-GlcpNSO36SO3]{[(4+1)][a-L-IdopA2SO3]{[(4+1)][a-D-GlcpNSO36SO3]{[(4+1)][a-L-IdopA2SO3]{[(4+1)][a-D-GlcpNSO36SO3]{[(3+1)][a-L-IdopA2SO3]{}}}}}}}}LINUCSPDB-CARE
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.21 Å3/Da / Density % sol: 70.77 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.1 M bis-Tris pH 6.5, 0.2 M sodium citrate and 20% w/v PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97631 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 22, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97631 Å / Relative weight: 1
ReflectionResolution: 2.7→147.6 Å / Num. obs: 71834 / % possible obs: 99.9 % / Redundancy: 6.6 % / CC1/2: 1 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.033 / Net I/σ(I): 12.6
Reflection shellResolution: 2.7→2.75 Å / Redundancy: 5.8 % / Mean I/σ(I) obs: 0.8 / Num. unique obs: 3487 / CC1/2: 0.3 / % possible all: 98.4

-
Processing

Software
NameVersionClassification
PHENIX(dev_2645: ???)refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2WFT

2wft


Resolution: 2.7→84.855 Å / SU ML: 0.52 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 29.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2398 3635 5.13 %
Rwork0.2158 --
obs0.217 70890 98.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7→84.855 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10168 0 141 0 10309
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00410572
X-RAY DIFFRACTIONf_angle_d0.86614323
X-RAY DIFFRACTIONf_dihedral_angle_d18.1786420
X-RAY DIFFRACTIONf_chiral_restr0.0511555
X-RAY DIFFRACTIONf_plane_restr0.0051843
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.73540.53551340.47362314X-RAY DIFFRACTION90
2.7354-2.77290.50431370.46912466X-RAY DIFFRACTION94
2.7729-2.81250.45821220.44782490X-RAY DIFFRACTION96
2.8125-2.85450.4341510.41182515X-RAY DIFFRACTION97
2.8991-2.94660.39031420.38322613X-RAY DIFFRACTION98
2.9466-2.99740.41191340.37152509X-RAY DIFFRACTION98
2.9974-3.05190.39471390.33812615X-RAY DIFFRACTION99
3.0519-3.11060.3341390.31632592X-RAY DIFFRACTION99
3.1106-3.17410.32641470.30942575X-RAY DIFFRACTION99
3.1741-3.24320.33271560.31772601X-RAY DIFFRACTION99
3.2432-3.31860.35921250.27782598X-RAY DIFFRACTION99
3.3186-3.40160.28671440.24522589X-RAY DIFFRACTION100
3.4016-3.49360.29011360.22952640X-RAY DIFFRACTION100
3.4936-3.59640.2331360.21412605X-RAY DIFFRACTION100
3.5964-3.71250.24711440.20972652X-RAY DIFFRACTION100
3.7125-3.84520.22151550.19672567X-RAY DIFFRACTION100
3.8452-3.99910.20171270.19052652X-RAY DIFFRACTION100
3.9991-4.18110.22291440.17592633X-RAY DIFFRACTION100
4.1811-4.40150.16481470.15522585X-RAY DIFFRACTION100
4.4015-4.67730.16091650.1442598X-RAY DIFFRACTION100
4.6773-5.03840.17571420.14322650X-RAY DIFFRACTION100
5.0384-5.54530.20091130.15682667X-RAY DIFFRACTION100
5.5453-6.34750.20791170.18762655X-RAY DIFFRACTION100
6.3475-7.99630.21741350.2112662X-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)
13.6880.86280.30882.7779-0.674.80190.3621-0.9789-0.01570.7452-0.3189-0.2173-0.10910.6617-0.04680.5293-0.08370.00750.9427-0.07460.5323-60.276624.265672.4728
28.64193.61555.50475.25434.22619.0242-0.0682-1.56220.2981.1752-0.24720.77310.3782-0.37370.35620.9325-0.18330.24721.3776-0.010.6547-75.512425.262481.4185
32.49581.27050.69365.2722-0.04944.84440.2876-0.70360.1910.4095-0.02660.45530.0756-0.6857-0.24430.3878-0.00880.130.7102-0.01410.5848-74.583221.536759.026
49.24557.59647.26117.76457.26726.88510.14220.197-0.63970.1463-0.219-0.18511.5056-0.9528-0.1721.1102-0.3299-0.06811.1284-0.18090.7601-39.743249.304489.0873
53.5497-0.2554-0.71064.97750.93035.64350.03580.0571-0.38250.0302-0.0038-0.35730.75740.4078-0.03950.50240.1443-0.08820.3918-0.02340.5013-60.832510.281232.2529
63.33320.5059-0.40795.4905-0.03874.8552-0.06080.7517-0.2682-1.46650.0699-0.22520.86640.1010.05911.06540.1632-0.01640.6737-0.17180.6433-60.54838.085311.8733
75.4614-1.5646-0.4014.87042.06892.08870.38610.85320.1459-1.3505-0.39350.0891-0.478-0.08160.13850.91550.22320.03920.74970.05170.726-63.222328.012114.7751
80.9004-0.70872.29694.8661-4.71948.77430.20370.39610.2989-0.4356-0.06020.5213-0.5854-0.2647-0.19050.58690.24470.02730.4827-0.03830.639-69.116732.64124.7209
93.51471.2709-0.98245.09211.40315.7470.2249-0.2153-0.35760.0965-0.1285-0.29390.43920.0771-0.03030.43240.127-0.08890.33780.06550.5287-67.039118.814136.2899
100.62921.30181.20545.70792.27911.7586-0.0978-0.41820.27950.1568-0.1915-0.4455-1.19170.27080.10461.2118-0.2287-0.03280.7218-0.22630.8883-69.287-24.35278.61
118.4419-1.8274-3.85596.46022.00138.079-0.04320.32840.2751-0.06860.17070.2156-0.1761-0.412-0.13540.3388-0.0052-0.06680.29030.0930.4172-2.74248.849711.2257
123.6398-0.68040.25852.74690.27965.0657-0.1972-0.92950.48710.46480.23740.015-0.8193-0.5639-0.04020.6220.22340.06110.6573-0.12890.7076-8.868716.776129.0809
138.71091.3245-3.25749.6372-1.41249.51510.0372-1.5741-0.68210.661-0.1291-0.3036-0.42910.15910.1060.54550.1875-0.05770.88630.03930.6114-0.85163.677337.6112
145.0871-0.1556-0.14465.74110.65632.44380.3497-1.3438-0.91940.84110.6008-1.12780.27011.2873-0.5140.58720.1065-0.15651.1437-0.15120.881911.62264.317529.1439
152.35760.8557-0.13833.1298-1.33055.7044-0.1581-0.158-0.21910.11990.0087-0.17680.33530.51020.15390.36030.08970.01580.362-0.0060.62576.49261.432315.6419
165.8963-2.1943-2.94912.53781.65335.7779-0.10290.46680.18220.14020.14490.2104-0.198-0.52670.11640.32810.1017-0.09350.35440.10260.513-5.87916.86958.9883
176.9862-6.6949-6.39068.31816.41695.8145-0.5368-0.3486-0.14720.0979-0.32880.10470.943-0.46831.01310.7360.2360.24241.458-0.08711.0484-32.927216.021435.5899
184.04723.66592.13917.0756-0.83823.29620.3198-0.25260.67330.1916-0.1377-0.2284-0.58121.0589-0.14430.48590.06660.09310.8097-0.1340.7963-48.460332.167342.2106
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'C' and (resid 213 through 400 )
2X-RAY DIFFRACTION2chain 'C' and (resid 401 through 478 )
3X-RAY DIFFRACTION3chain 'C' and (resid 479 through 606 )
4X-RAY DIFFRACTION4chain 'C' and (resid 607 through 670 )
5X-RAY DIFFRACTION5chain 'A' and (resid 214 through 283 )
6X-RAY DIFFRACTION6chain 'A' and (resid 284 through 435 )
7X-RAY DIFFRACTION7chain 'A' and (resid 436 through 496 )
8X-RAY DIFFRACTION8chain 'A' and (resid 497 through 535 )
9X-RAY DIFFRACTION9chain 'A' and (resid 536 through 606 )
10X-RAY DIFFRACTION10chain 'A' and (resid 607 through 670 )
11X-RAY DIFFRACTION11chain 'B' and (resid 214 through 241 )
12X-RAY DIFFRACTION12chain 'B' and (resid 242 through 410 )
13X-RAY DIFFRACTION13chain 'B' and (resid 411 through 454 )
14X-RAY DIFFRACTION14chain 'B' and (resid 455 through 496 )
15X-RAY DIFFRACTION15chain 'B' and (resid 497 through 567 )
16X-RAY DIFFRACTION16chain 'B' and (resid 568 through 606 )
17X-RAY DIFFRACTION17chain 'B' and (resid 607 through 640 )
18X-RAY DIFFRACTION18chain 'B' and (resid 641 through 670 )

+
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