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- PDB-6o5e: Crystal structure of the Vitronectin hemopexin-like domain -

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Basic information

Entry
Database: PDB / ID: 6o5e
TitleCrystal structure of the Vitronectin hemopexin-like domain
ComponentsVitronectin
KeywordsCELL ADHESION / integrin ligand / hemopexin-like domain / beta-propeller / serum protein
Function / homology
Function and homology information


smooth muscle cell-matrix adhesion / rough endoplasmic reticulum lumen / peptidase inhibitor complex / alphav-beta3 integrin-vitronectin complex / protein complex involved in cell-matrix adhesion / positive regulation of vascular endothelial growth factor signaling pathway / extracellular matrix binding / positive regulation of vascular endothelial growth factor receptor signaling pathway / positive regulation of cell-substrate adhesion / extracellular matrix structural constituent ...smooth muscle cell-matrix adhesion / rough endoplasmic reticulum lumen / peptidase inhibitor complex / alphav-beta3 integrin-vitronectin complex / protein complex involved in cell-matrix adhesion / positive regulation of vascular endothelial growth factor signaling pathway / extracellular matrix binding / positive regulation of vascular endothelial growth factor receptor signaling pathway / positive regulation of cell-substrate adhesion / extracellular matrix structural constituent / positive regulation of smooth muscle cell migration / scavenger receptor activity / Molecules associated with elastic fibres / cell adhesion mediated by integrin / Syndecan interactions / positive regulation of wound healing / endodermal cell differentiation / polysaccharide binding / oligodendrocyte differentiation / basement membrane / negative regulation of blood coagulation / protein polymerization / negative regulation of fibrinolysis / ECM proteoglycans / Integrin cell surface interactions / regulation of cell adhesion / collagen binding / negative regulation of proteolysis / extracellular matrix organization / liver regeneration / Regulation of Complement cascade / cell-matrix adhesion / integrin-mediated signaling pathway / positive regulation of receptor-mediated endocytosis / Golgi lumen / integrin binding / cell migration / heparin binding / : / blood microparticle / cell adhesion / immune response / intracellular membrane-bounded organelle / endoplasmic reticulum / extracellular space / extracellular exosome / extracellular region / identical protein binding
Similarity search - Function
: / Somatomedin B domain, chordata / Hemopexin, conserved site / Hemopexin domain signature. / Hemopexin-like domain / Somatomedin B -like domains / Somatomedin B domain / Somatomedin B-like domain superfamily / Somatomedin B domain / Somatomedin B domain (SMB) signature. ...: / Somatomedin B domain, chordata / Hemopexin, conserved site / Hemopexin domain signature. / Hemopexin-like domain / Somatomedin B -like domains / Somatomedin B domain / Somatomedin B-like domain superfamily / Somatomedin B domain / Somatomedin B domain (SMB) signature. / Somatomedin B (SMB) domain profile. / Hemopexin-like repeats / Hemopexin-like domain superfamily / Hemopexin / Hemopexin repeat profile. / Hemopexin-like repeats.
Similarity search - Domain/homology
IMIDAZOLE / NITRATE ION / Vitronectin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsLechtenberg, B.C. / Shin, K. / Marassi, F.M.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM118186 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)P30CA030199 United States
CitationJournal: Sci Adv / Year: 2019
Title: Structure of human Vitronectin C-terminal domain and interaction withYersinia pestisouter membrane protein Ail.
Authors: Shin, K. / Lechtenberg, B.C. / Fujimoto, L.M. / Yao, Y. / Bartra, S.S. / Plano, G.V. / Marassi, F.M.
History
DepositionMar 1, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 2, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _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_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
Revision 1.4Oct 30, 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: Vitronectin
B: Vitronectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,45513
Polymers46,8722
Non-polymers58211
Water3,027168
1
A: Vitronectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6836
Polymers23,4361
Non-polymers2475
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Vitronectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7727
Polymers23,4361
Non-polymers3366
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.560, 97.360, 49.160
Angle α, β, γ (deg.)90.000, 99.900, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLUASPASP(chain 'A' and (resid 154 through 184 or resid 193...AA154 - 1842 - 32
12PROPROILEILE(chain 'A' and (resid 154 through 184 or resid 193...AA193 - 21341 - 61
13GLYGLYPROPRO(chain 'A' and (resid 154 through 184 or resid 193...AA217 - 24065 - 88
14ASNASNPROPRO(chain 'A' and (resid 154 through 184 or resid 193...AA242 - 26190 - 109
15GLUGLUPHEPHE(chain 'A' and (resid 154 through 184 or resid 193...AA269 - 284117 - 132
16GLNGLNILEILE(chain 'A' and (resid 154 through 184 or resid 193...AA331 - 354141 - 164
17SERSERALAALA(chain 'A' and (resid 154 through 184 or resid 193...AA435 - 474165 - 204
28GLUGLUASPASP(chain 'B' and (resid 154 through 240 or resid 242 through 474 or resid 501 through 504))BB154 - 1842 - 32
29PROPROILEILE(chain 'B' and (resid 154 through 240 or resid 242 through 474 or resid 501 through 504))BB193 - 21341 - 61
210GLYGLYPROPRO(chain 'B' and (resid 154 through 240 or resid 242 through 474 or resid 501 through 504))BB217 - 24065 - 88
211ASNASNPROPRO(chain 'B' and (resid 154 through 240 or resid 242 through 474 or resid 501 through 504))BB242 - 26190 - 109
212GLUGLUPHEPHE(chain 'B' and (resid 154 through 240 or resid 242 through 474 or resid 501 through 504))BB269 - 284117 - 132
213GLNGLNILEILE(chain 'B' and (resid 154 through 240 or resid 242 through 474 or resid 501 through 504))BB331 - 354141 - 164
214SERSERALAALA(chain 'B' and (resid 154 through 240 or resid 242 through 474 or resid 501 through 504))BB435 - 474165 - 204

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Vitronectin / VN / S-protein / Serum-spreading factor / V75


Mass: 23436.197 Da / Num. of mol.: 2
Fragment: hemopexin-like domain (UNP residues 154-285, 324-354, 435-474)
Mutation: C180S, C215S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VTN / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P04004

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Non-polymers , 6 types, 179 molecules

#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#6: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 168 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.04 Å3/Da / Density % sol: 39.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 1 uL protein solution + 1 uL precipitate solution [0.09 M imidazole/MES, pH 6.5, 27 mM sodium nitrate, 27 mM sodium phosphate dibasic, 27 mM ammonium sulfate, 11.25% v/v MPD, 11.25% w/v ...Details: 1 uL protein solution + 1 uL precipitate solution [0.09 M imidazole/MES, pH 6.5, 27 mM sodium nitrate, 27 mM sodium phosphate dibasic, 27 mM ammonium sulfate, 11.25% v/v MPD, 11.25% w/v PEG1000, 11.25% w/v PEG3350, 3% w/v D-(+)-trehalose]

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Jan 3, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→26.96 Å / Num. obs: 29017 / % possible obs: 98.1 % / Redundancy: 2.3 % / Biso Wilson estimate: 27 Å2 / CC1/2: 0.988 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.055 / Rrim(I) all: 0.088 / Net I/σ(I): 7.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.9-1.942.30.389219150.8370.3220.50696.1
8.91-26.962.20.03912.82790.9930.0320.05191.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.14rc2-3191refinement
MOSFLM7.2.2data reduction
Aimless0.7.3data scaling
PHASERphasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 1QHU, 1RTG, 2MQS, 3C7X, 4RT6

1qhu

1rtg

2mqs

3c7x

4rt6


Resolution: 1.9→24.21 Å / SU ML: 0.2099 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.1039
RfactorNum. reflection% reflection
Rfree0.2102 1472 5.08 %
Rwork0.1793 --
obs0.1809 28986 97.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 39.97 Å2
Refinement stepCycle: LAST / Resolution: 1.9→24.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3001 0 30 168 3199
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00463131
X-RAY DIFFRACTIONf_angle_d0.83214242
X-RAY DIFFRACTIONf_chiral_restr0.0481405
X-RAY DIFFRACTIONf_plane_restr0.0054558
X-RAY DIFFRACTIONf_dihedral_angle_d9.19261803
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.960.2941280.24812453X-RAY DIFFRACTION96.27
1.96-2.030.24591190.21132484X-RAY DIFFRACTION96.26
2.03-2.110.22441320.20172447X-RAY DIFFRACTION97.39
2.11-2.210.21361270.19092492X-RAY DIFFRACTION97.32
2.21-2.330.2531400.20182479X-RAY DIFFRACTION97.54
2.33-2.470.23131280.19522509X-RAY DIFFRACTION98.14
2.47-2.660.23081160.20132530X-RAY DIFFRACTION98.51
2.66-2.930.24331400.19682526X-RAY DIFFRACTION98.7
2.93-3.350.21551470.18062503X-RAY DIFFRACTION98.92
3.35-4.220.18271480.1522551X-RAY DIFFRACTION99.45
4.22-24.220.1861470.15922540X-RAY DIFFRACTION98.28
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)
12.07498007788-0.293643819838-0.5498508064020.8136396580910.7707392317562.418358782150.007409229862440.323663895440.0379032769527-0.38720897244-0.1905384578120.1406119836530.0466089588434-0.313039289475-0.0009677066255990.281447683972-0.00339716864979-0.05698629409630.299858111530.02958260752690.3047214567376.7833279005846.317023588834.892739322
21.08043278790.2970855361440.7245818558610.2003353636120.07216752193811.15680452773-0.437914882472-0.567810323280.6548089944530.06662608380330.3373422483530.230729425594-0.7107769201-0.512601374677-0.01350930652350.281810231730.0786726300534-0.06050802813660.3696315477780.04253231870890.3421767343381.0708182406852.929537482843.3512904808
33.716511103560.53902671355-0.8653663082112.096962769890.2652912363222.58544775062-0.0649624933506-0.5746758231590.03210155305840.3015327012940.0202762651191-0.08949055647330.148332219280.149535213337-0.01248215853220.256244876630.0385178989262-0.05436324668030.3033386652710.01163915240160.20852481257613.213046364147.812798333853.6331303319
41.94928085585-0.729968241591-0.5588469276610.331313437858-0.1772777790272.73519569317-0.04816883071030.112613481134-0.08187707321810.2267894734140.0710736815285-0.152965000604-0.2303033643040.3110504534520.0003734258450450.234606335036-0.0075958804033-0.02503615133010.2297592553690.04121624767060.2900410260322.806510151546.652568065141.8632131762
52.752351380681.19661041172-0.4126827021362.936861007511.024145965272.871278120410.02385665880450.390749530108-0.28690489668-0.330475289876-0.0269961547185-0.4498095190390.1679887750740.7021232640180.02245553159240.241558159489-0.03522505622040.003634816014660.3238231955970.03233549254750.2847999090124.51891310144.802483621633.3055212941
60.6284481457070.523758266667-0.1716614670840.697389024850.0392374792360.693163687892-0.0588261313188-0.302034522588-0.4783499308680.65269855206-0.1007303511130.832940854291-0.131933916602-0.310146960292-0.0003350779706260.4687407553090.02095816317230.04141643876280.295717071373-0.01093584605030.4973120444214.3012584310722.852303782929.3254230387
71.029768862910.1517081949610.7659540490150.407875923604-0.1476638656840.7677939410640.076427056322-0.409563863755-0.6215076020140.750622035997-0.006956024997020.8078900677320.319441127782-0.35525114980.01599921986490.517493351776-0.03552139785530.1513579888360.3998555749320.01281324017490.584221520681-0.83044761523316.295993092728.9056759047
80.6565246843250.4792096717630.1890197874180.4922290148470.584028357061.451533737690.08017417412370.198469740772-0.364579251985-0.557594600927-0.4985848201851.33983770785-0.0591131898549-0.309602567013-0.06042101211840.3018217931310.0432810748701-0.06955714948850.280485274718-0.1000742543970.468421420718-2.5406364080322.334655997316.7164580112
90.6224987933320.3337224344230.06808422632291.00161511762-0.908976079651.146378139190.1862285787890.196108219561-0.219691629142-0.310863752986-0.006617229679010.94832477385-0.0290066996216-0.4608520222450.02200866168240.377685876290.03391699295-0.07137012579930.399836935601-0.1585431368870.711378846183-7.508527010115.751278153614.7347559581
102.15714461134-0.0179412686436-0.3246564431681.89118544432-0.7774707857131.01277594780.2333063628190.591822719852-0.156163943452-0.948665030061-0.0389827977078-0.162260409144-0.26050298741-0.02345378426960.1303643700330.5543428969620.07166776351050.09781563270330.362035372243-0.02758963343850.2863996034128.4937179181923.37557298169.55605501127
111.496641689521.657312399980.8279364608962.228568672920.1971669387181.77321714993-0.13295767933-0.0150055739715-0.0723658090942-0.4683052644060.117088613327-0.4562561706310.1535930089350.1237977696970.0003005993809010.2868586743910.03133310782720.04962494490160.268020272928-0.02499537499020.31911183382611.893899004829.084744376520.4067493093
120.9147023478271.00589842567-0.07007488603581.299583907110.09572711923670.15932422460.08059245856880.200873607195-0.245371616312-0.245241768884-0.0908240830891-0.2860263967490.210988668850.304016683157-0.0002913052310970.336854526807-0.01136584751740.007652059709630.253807922074-0.001221444722410.25165182805715.400034777335.0689004922.5204780104
130.411848874416-0.211658873309-0.1643169277880.45992443211-0.02822057793420.260551439020.0931856832474-0.361978577376-0.2253154229970.998099884026-0.184885823482-0.3136606149310.2551240923120.1487755079590.0007014995853880.506023292368-0.0674227598776-0.01462440245360.2556747271670.03175901751970.34111080361113.7041951730.091425438334.3901753979
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 153 through 195 )
2X-RAY DIFFRACTION2chain 'A' and (resid 196 through 207 )
3X-RAY DIFFRACTION3chain 'A' and (resid 208 through 338 )
4X-RAY DIFFRACTION4chain 'A' and (resid 339 through 440 )
5X-RAY DIFFRACTION5chain 'A' and (resid 441 through 474 )
6X-RAY DIFFRACTION6chain 'B' and (resid 154 through 171 )
7X-RAY DIFFRACTION7chain 'B' and (resid 172 through 207 )
8X-RAY DIFFRACTION8chain 'B' and (resid 208 through 223 )
9X-RAY DIFFRACTION9chain 'B' and (resid 224 through 242 )
10X-RAY DIFFRACTION10chain 'B' and (resid 243 through 338 )
11X-RAY DIFFRACTION11chain 'B' and (resid 339 through 440 )
12X-RAY DIFFRACTION12chain 'B' and (resid 441 through 458 )
13X-RAY DIFFRACTION13chain 'B' and (resid 459 through 474 )

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