[English] 日本語
Yorodumi
- PDB-4dy0: Crystal structure of native protease nexin-1 with heparin -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4dy0
TitleCrystal structure of native protease nexin-1 with heparin
ComponentsGlia-derived nexin
KeywordsHYDROLASE INHIBITOR / serpin / protease inhibitor / thrombin / cell surface
Function / homology
Function and homology information


cerebellar granular layer morphogenesis / mating plug formation / seminal vesicle epithelium development / regulation of timing of cell differentiation / secretory granule organization / negative regulation of sodium ion transport / detection of mechanical stimulus involved in sensory perception / secretion by cell / positive regulation of astrocyte differentiation / innervation ...cerebellar granular layer morphogenesis / mating plug formation / seminal vesicle epithelium development / regulation of timing of cell differentiation / secretory granule organization / negative regulation of sodium ion transport / detection of mechanical stimulus involved in sensory perception / secretion by cell / positive regulation of astrocyte differentiation / innervation / platelet alpha granule / negative regulation of platelet aggregation / negative regulation of plasminogen activation / glycosaminoglycan binding / negative regulation of blood coagulation / Dissolution of Fibrin Clot / negative regulation of protein processing / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / negative regulation of smoothened signaling pathway / Common Pathway of Fibrin Clot Formation / regulation of cell migration / regulation of synaptic transmission, glutamatergic / Intrinsic Pathway of Fibrin Clot Formation / long-term synaptic potentiation / negative regulation of proteolysis / protein catabolic process / serine-type endopeptidase inhibitor activity / neuromuscular junction / negative regulation of cell growth / negative regulation of protein catabolic process / platelet activation / extracellular vesicle / heparin binding / collagen-containing extracellular matrix / cell differentiation / negative regulation of cell population proliferation / signaling receptor binding / extracellular space / extracellular region / cytosol
Similarity search - Function
Antithrombin; Chain I, domain 2 / Antithrombin, subunit I, domain 2 / Alpha-1-antitrypsin; domain 1 / Alpha-1-antitrypsin, domain 1 / Serpin, conserved site / Serpins signature. / Serpin superfamily, domain 2 / Serpin family / Serpin domain / Serpin superfamily ...Antithrombin; Chain I, domain 2 / Antithrombin, subunit I, domain 2 / Alpha-1-antitrypsin; domain 1 / Alpha-1-antitrypsin, domain 1 / Serpin, conserved site / Serpins signature. / Serpin superfamily, domain 2 / Serpin family / Serpin domain / Serpin superfamily / Serpin superfamily, domain 1 / Serpin (serine protease inhibitor) / SERine Proteinase INhibitors / Roll / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsHuntington, J.A. / Li, W.
CitationJournal: Blood / Year: 2012
Title: Crystal structures of protease nexin-1 in complex with heparin and thrombin suggest a 2-step recognition mechanism.
Authors: Li, W. / Huntington, J.A.
History
DepositionFeb 28, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 15, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2015Group: Non-polymer description
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_src_nat / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_atoms / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity_src_nat.entity_id / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_value_order / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Feb 28, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Mar 13, 2024Group: Source and taxonomy / Structure summary / Category: entity / entity_src_nat / Item: _entity.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Glia-derived nexin
B: Glia-derived nexin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,9959
Polymers83,8312
Non-polymers1,1647
Water4,468248
1
A: Glia-derived nexin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,6994
Polymers41,9151
Non-polymers7843
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glia-derived nexin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,2965
Polymers41,9151
Non-polymers3804
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3460 Å2
ΔGint-54 kcal/mol
Surface area28960 Å2
MethodPISA
4
A: Glia-derived nexin
hetero molecules

B: Glia-derived nexin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,9959
Polymers83,8312
Non-polymers1,1647
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_544y+1/2,-x-1/2,z-1/41
Buried area2950 Å2
ΔGint-62 kcal/mol
Surface area29480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)140.650, 140.650, 93.550
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

-
Components

#1: Protein Glia-derived nexin / GDN / Peptidase inhibitor 7 / PI-7 / Protease nexin 1 / PN-1 / Protease nexin I / Serpin E2


Mass: 41915.488 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SERPINE2, PI7, PN1 / Production host: Escherichia coli (E. coli) / References: UniProt: P07093
#2: Polysaccharide 2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid


Type: oligosaccharide / Mass: 595.486 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/2,2,1/[a2121A-1a_1-5_2*OSO/3=O/3=O][a2122h-1a_1-5_2*NSO/3=O/3=O_6*OSO/3=O/3=O]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][a-L-IdopA2SO3]{[(4+1)][a-D-4-deoxy-GlcpNSO36SO3]{}}LINUCSPDB-CARE
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4 / Details: mucosal heparin
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 248 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.76 Å3/Da / Density % sol: 55.43 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 25mM NaAc, 12% PEG3350, 0.2M (NH4)2SO4, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 295K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 4, 2009
RadiationMonochromator: Si(111) double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.35→68.14 Å / Num. all: 39468 / Num. obs: 39468 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Biso Wilson estimate: 42.61 Å2 / Rmerge(I) obs: 0.138 / Rsym value: 0.128 / Net I/σ(I): 11.1
Reflection shellResolution: 2.35→2.48 Å / Mean I/σ(I) obs: 2.5 / % possible all: 100

-
Processing

Software
NameVersionClassification
DNAdata collection
PHASERphasing
REFMAC5.6.0098refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→68.14 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.936 / SU B: 12.461 / SU ML: 0.146 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.285 / ESU R Free: 0.215 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.22634 1976 5 %RANDOM
Rwork0.18174 ---
all0.1839 37395 --
obs0.1839 37395 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.913 Å2
Baniso -1Baniso -2Baniso -3
1--0.35 Å20 Å20 Å2
2---0.35 Å2-0 Å2
3---0.7 Å2
Refinement stepCycle: LAST / Resolution: 2.35→68.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5580 0 67 248 5895
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0225764
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.8351.9687852
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0355727
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.32324.818220
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.88715951
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3731522
X-RAY DIFFRACTIONr_chiral_restr0.0570.2940
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0214226
X-RAY DIFFRACTIONr_gen_planes_other
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.354→2.415 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.352 139 -
Rwork0.276 2514 -
obs--99.92 %
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)
11.0879-0.2717-0.52330.53970.53010.60.0358-0.059-0.06910.0782-0.0557-0.00770.048-0.07040.01980.0664-0.0076-0.04940.15680.02090.045421.8289-51.721649.4153
21.554-0.6109-0.10562.68711.29590.7067-0.0701-0.2815-0.33810.5459-0.02270.20070.31330.0510.09280.29320.0282-0.00750.24950.13010.120426.9202-62.801559.5346
35.96271.2434-3.74170.51990.21796.91410.0399-0.25040.48110.04980.15660.11630.03410.3765-0.19650.18160.0675-0.03890.4388-0.00260.051125.5897-46.98568.1039
43.80484.774-1.140313.8958-2.71182.94260.2571-0.8454-0.14431.03720.0562-0.1385-0.30730.4079-0.31330.2038-0.03170.01720.4568-0.03270.067129.7375-44.609866.2342
55.286-6.5353-3.329611.03435.25073.7302-0.0463-0.2072-0.11260.65270.1162-0.6126-0.15090.5256-0.06980.2695-0.1242-0.21140.45080.02280.229739.8737-43.223861.5994
612.4528-22.0135-5.890647.152413.06523.64130.5422-0.22890.0795-0.9548-0.4883-0.0757-0.2506-0.1526-0.05390.2441-0.00520.03520.4988-0.08740.104837.4431-38.199854.9347
73.8267-2.8086-1.77554.85812.65362.51490.0536-0.47340.334-0.02540.0710.0032-0.29890.3252-0.12460.185-0.0172-0.00810.2486-0.0680.165531.8402-43.334657.3908
81.4671-0.4795-0.49351.2864-1.16052.47660.0353-0.1341-0.094-0.0480.0169-0.0670.24310.0854-0.05230.06960.0044-0.05580.01510.00770.06640.0633-62.010334.8469
94.5614-0.9958-1.2714.7740.08591.6361-0.0172-0.0644-0.1187-0.14890.04570.28080.2763-0.0877-0.02850.1912-0.0289-0.08330.06470.04010.06730.8082-68.473136.0022
102.6329-0.5572-1.25040.4272-0.04361.11280.1606-0.2930.27260.0140.0551-0.0722-0.10870.0338-0.21560.04480.0073-0.01170.1382-0.00620.086724.6712-44.586951.1357
110.9166-0.0764-0.5590.81340.46351.65860.0646-0.2215-0.0713-0.00420.0194-0.0480.18420.119-0.0840.0636-0.0029-0.03880.07330.00630.034836.1429-56.798943.5912
122.70622.20582.33853.38972.52393.91650.0651-0.2038-0.13250.1073-0.1470.1010.25730.00140.08190.02440.01530.02670.03390.0320.115414.2122-42.834126.3124
131.5485-0.8741-1.10150.52430.63581.0750.08070.1571-0.1624-0.0848-0.09570.12610.0288-0.19590.01510.0962-0.0276-0.08270.059-0.00550.115512.3963-45.594911.6563
144.86780.8845-3.74984.19560.26983.1420.09760.2184-0.0032-0.6429-0.10030.0823-0.1687-0.18880.00270.22960.046-0.06220.0752-0.0080.021519.2936-43.48060.7657
153.3876-1.2394-1.81175.22130.954.703-0.18760.26430.3166-0.36480.09970.1373-0.08840.10130.08790.1267-0.0405-0.00790.04310.05140.085524.8816-29.60026.3392
1632.0009-12.4637-8.483321.19974.29963.65310.179-0.1878-0.5572-0.078-0.1122-0.45170.2149-0.0265-0.06680.13940.0013-0.02020.01270.02120.062731.3701-31.128413.0309
171.5551-1.2445-0.13761.49730.71941.04310.2076-0.00670.1585-0.2565-0.06-0.1126-0.2445-0.0841-0.14750.09780.00190.05710.02330.0280.154610.7532-26.27524.5966
180.8557-0.11790.13670.60070.17081.0940.0678-0.1673-0.01960.0302-0.00480.0453-0.0166-0.11-0.0630.0099-0.0140.00490.05950.02710.08914.2485-33.090636.1009
191.65-0.7884-1.05691.49860.48330.91190.0031-0.0940.0504-0.0190.10240.07970.05520.0274-0.10540.03880.0119-0.03990.05410.010.06059.246-38.202528.9896
204.6975-0.49192.03163.2771-0.14526.88840.07460.2452-0.2091-0.46140.0094-0.13180.30410.1359-0.08410.15490.00240.02080.0238-0.03220.05429.7725-51.66096.9955
210.82750.2589-0.19770.0892-0.09680.29560.07530.0270.11440.02570.00470.0413-0.093-0.0357-0.08010.05390.02870.01780.02560.02380.09434.5164-28.579528.3097
220.8969-0.1362-0.52771.03091.6682.84470.0641-0.1369-0.06190.0407-0.0593-0.02360.0546-0.0606-0.00480.0166-0.0110.00330.04840.04470.12728.0909-33.900929.1465
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 62
2X-RAY DIFFRACTION2A63 - 89
3X-RAY DIFFRACTION3A90 - 112
4X-RAY DIFFRACTION4A113 - 126
5X-RAY DIFFRACTION5A127 - 145
6X-RAY DIFFRACTION6A146 - 154
7X-RAY DIFFRACTION7A155 - 171
8X-RAY DIFFRACTION8A172 - 251
9X-RAY DIFFRACTION9A252 - 272
10X-RAY DIFFRACTION10A273 - 309
11X-RAY DIFFRACTION11A310 - 379
12X-RAY DIFFRACTION12B4 - 34
13X-RAY DIFFRACTION13B35 - 96
14X-RAY DIFFRACTION14B97 - 120
15X-RAY DIFFRACTION15B121 - 146
16X-RAY DIFFRACTION16B147 - 157
17X-RAY DIFFRACTION17B158 - 192
18X-RAY DIFFRACTION18B193 - 251
19X-RAY DIFFRACTION19B252 - 295
20X-RAY DIFFRACTION20B296 - 315
21X-RAY DIFFRACTION21B316 - 352
22X-RAY DIFFRACTION22B353 - 379

+
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