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- PDB-1us1: Crystal structure of human vascular adhesion protein-1 -

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Basic information

Entry
Database: PDB / ID: 1us1
TitleCrystal structure of human vascular adhesion protein-1
ComponentsMEMBRANE COPPER AMINE OXIDASE
KeywordsOXIDASE / COPPER AMINE OXIDASE / VASCULAR ADHESION PROTEIN-1
Function / homology
Function and homology information


primary-amine oxidase / aliphatic amine oxidase activity / primary amine oxidase activity / amine metabolic process / Phase I - Functionalization of compounds / microvillus / quinone binding / early endosome / cell adhesion / inflammatory response ...primary-amine oxidase / aliphatic amine oxidase activity / primary amine oxidase activity / amine metabolic process / Phase I - Functionalization of compounds / microvillus / quinone binding / early endosome / cell adhesion / inflammatory response / copper ion binding / protein heterodimerization activity / response to antibiotic / calcium ion binding / Golgi apparatus / cell surface / endoplasmic reticulum / identical protein binding / membrane / plasma membrane / cytoplasm
Similarity search - Function
Copper amine oxidase, N3-terminal / Copper amine oxidase, N2-terminal / Copper amine oxidase, N2 domain / Copper amine oxidase, N3 domain / Copper amine oxidase, catalytic domain / Copper amine oxidase copper-binding site signature. / Copper amine oxidase topaquinone signature. / Nuclear Transport Factor 2; Chain: A, - #40 / Copper amine oxidase / Copper amine oxidase, catalytic domain ...Copper amine oxidase, N3-terminal / Copper amine oxidase, N2-terminal / Copper amine oxidase, N2 domain / Copper amine oxidase, N3 domain / Copper amine oxidase, catalytic domain / Copper amine oxidase copper-binding site signature. / Copper amine oxidase topaquinone signature. / Nuclear Transport Factor 2; Chain: A, - #40 / Copper amine oxidase / Copper amine oxidase, catalytic domain / Copper amine oxidase, N-terminal / Copper amine oxidase, catalytic domain superfamily / Copper amine oxidase, enzyme domain / Beta-galactosidase; Chain A, domain 5 / Nuclear Transport Factor 2; Chain: A, / Distorted Sandwich / Roll / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
COPPER (II) ION / Amine oxidase [copper-containing] 3
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsAirenne, T.T. / Nymalm, Y. / Kidron, H. / Soderholm, A. / Johnson, M.S. / Salminen, T.A.
Citation
Journal: Protein Sci. / Year: 2005
Title: Crystal Structure of the Human Vascular Adhesion Protein-1: Unique Structural Features with Functional Implications.
Authors: Airenne, T.T. / Nymalm, Y. / Kidron, H. / Smith, D.J. / Pihlavisto, M. / Salmi, M. / Jalkanen, S. / Johnson, M.S. / Salminen, T.A.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2003
Title: Crystallization and Preliminary X-Ray Analysis of the Human Vascular Adhesion Protein-1
Authors: Nymalm, Y. / Kidron, H. / Soderholm, A. / Viitanen, L. / Kaukonen, K. / Pihlavisto, M. / Smith, D. / Veromaa, T. / Airenne, T.T. / Johnson, M.S. / Salminen, T.A.
History
DepositionNov 17, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 16, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 28, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / 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_struct_conn_angle / 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.name / _chem_comp.type / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 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
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MEMBRANE COPPER AMINE OXIDASE
B: MEMBRANE COPPER AMINE OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)171,04812
Polymers169,4692
Non-polymers1,57910
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)226.099, 226.099, 223.004
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1 / Refine code: 2

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLNGLNTYRTYRAA58 - 20158 - 201
21GLNGLNTYRTYRBB58 - 20158 - 201
12GLYGLYCYSCYSAA205 - 741205 - 741
22GLYGLYCYSCYSBB205 - 741205 - 741
13LEULEUSERSERAA752 - 761752 - 761
23LEULEUSERSERBB752 - 761752 - 761

NCS oper: (Code: given
Matrix: (-0.3685, 0.3581, 0.8579), (0.3561, -0.7981, 0.4861), (0.8587, 0.4846, 0.1665)
Vector: 2.7146, 226.99741, -96.2491)

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Components

#1: Protein MEMBRANE COPPER AMINE OXIDASE / VASCULAR ADHESION PROTEIN-1 / VAP-1


Mass: 84734.562 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: CRICETULUS GRISEUS (Chinese hamster) / References: UniProt: Q16853, EC: 1.4.3.6
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#5: 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


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
Compound detailsCELL ADHESION PROTEIN THAT BINDS TO LYMPHOCYTES. MONOAMINE OXIDASE ACTIVITY WITH COFACTORS OF ONE ...CELL ADHESION PROTEIN THAT BINDS TO LYMPHOCYTES. MONOAMINE OXIDASE ACTIVITY WITH COFACTORS OF ONE COPPER ION AND ONE TOPAQUINONE PER SUBUNIT.

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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: 4.6 Å3/Da / Density % sol: 73 %
Crystal growpH: 8 / Details: pH 8.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.95
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 15, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 2.9→20 Å / Num. obs: 69536 / % possible obs: 93.3 % / Redundancy: 10.4 % / Rmerge(I) obs: 0.121 / Net I/σ(I): 19
Reflection shellResolution: 2.9→3 Å / Redundancy: 10.4 % / Rmerge(I) obs: 0.474 / Mean I/σ(I) obs: 6.4 / % possible all: 95.3

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PU4

1pu4


Resolution: 2.9→19.96 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.887 / SU B: 15.68 / SU ML: 0.261 / Cross valid method: THROUGHOUT / ESU R: 0.512 / ESU R Free: 0.323 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.267 3476 5 %RANDOM
Rwork0.241 ---
obs0.242 69536 93.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 41.04 Å2
Baniso -1Baniso -2Baniso -3
1--5.68 Å2-2.84 Å20 Å2
2---5.68 Å20 Å2
3---8.52 Å2
Refinement stepCycle: LAST / Resolution: 2.9→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11063 0 90 0 11153
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.02111534
X-RAY DIFFRACTIONr_bond_other_d0.0020.0210053
X-RAY DIFFRACTIONr_angle_refined_deg1.8911.94615706
X-RAY DIFFRACTIONr_angle_other_deg0.99323285
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.82251398
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.10.21655
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212978
X-RAY DIFFRACTIONr_gen_planes_other0.0050.022531
X-RAY DIFFRACTIONr_nbd_refined0.2110.22141
X-RAY DIFFRACTIONr_nbd_other0.2340.211494
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0940.27078
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1770.2134
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3390.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2280.232
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1880.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5391.57012
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.041211253
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.57134522
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.7054.54453
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

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
4036tight positional0.070.05
6358medium positional0.420.5
4036tight thermal0.120.5
6358medium thermal0.582
LS refinement shellResolution: 2.9→2.97 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.419 253
Rwork0.404 4810

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