[English] 日本語
Yorodumi
- PDB-2r0l: Short Form HGFA with Inhibitory Fab75 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2r0l
TitleShort Form HGFA with Inhibitory Fab75
Components
  • (Hepatocyte growth factor ...) x 2
  • antibody heavy chain, Fab portion only
  • antibody light chain
KeywordsHYDROLASE / IMMUNE SYSTEM / serine protease / antibody / allosteric inhibitor / EGF-like domain / Glycoprotein / Kringle / Secreted / Zymogen
Function / homology
Function and homology information


MET Receptor Activation / zymogen activation / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / rough endoplasmic reticulum / serine-type peptidase activity / blood coagulation / serine-type endopeptidase activity / proteolysis / extracellular space / extracellular region / cytosol
Similarity search - Function
Coagulation factor XII/hepatocyte growth factor activator / Fibronectin, type I / Fibronectin type-I domain signature. / Fibronectin type-I domain profile. / Fibronectin type 1 domain / Fibronectin type II domain / Fibronectin type II domain superfamily / Fibronectin type II domain / Fibronectin type-II collagen-binding domain signature. / Fibronectin type-II collagen-binding domain profile. ...Coagulation factor XII/hepatocyte growth factor activator / Fibronectin, type I / Fibronectin type-I domain signature. / Fibronectin type-I domain profile. / Fibronectin type 1 domain / Fibronectin type II domain / Fibronectin type II domain superfamily / Fibronectin type II domain / Fibronectin type-II collagen-binding domain signature. / Fibronectin type-II collagen-binding domain profile. / Fibronectin type 2 domain / EGF-like domain / Kringle domain / Kringle / Kringle, conserved site / Kringle superfamily / Kringle domain signature. / Kringle domain profile. / Kringle domain / : / Kringle-like fold / Epidermal growth factor-like domain. / EGF-like domain profile. / EGF-like domain signature 1. / EGF-like domain signature 2. / EGF-like domain / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Immunoglobulins / Peptidase S1, PA clan / Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Hepatocyte growth factor activator serine protease
Similarity search - Component
Biological speciesHomo sapiens (human)
Synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsEigenbrot, C. / Shia, S.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2007
Title: Structural insight into distinct mechanisms of protease inhibition by antibodies.
Authors: Wu, Y. / Eigenbrot, C. / Liang, W.C. / Stawicki, S. / Shia, S. / Fan, B. / Ganesan, R. / Lipari, M.T. / Kirchhofer, D.
History
DepositionAug 20, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Sep 25, 2013Group: Source and taxonomy
Revision 1.3Oct 25, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / 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 / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 30, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 400COMPOUND CHAINS A AND B ARE PART OF THE HGFA SEQUENCE. IN THE MATURE PROTEIN STUDIED HERE, A ...COMPOUND CHAINS A AND B ARE PART OF THE HGFA SEQUENCE. IN THE MATURE PROTEIN STUDIED HERE, A PEPTIDE BOND HAS BEEN BROKEN AND THE TWO SEGMENTS REMAIN CONNECTED BY A DISULFIDE BOND.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
L: antibody light chain
H: antibody heavy chain, Fab portion only
A: Hepatocyte growth factor activator
B: Hepatocyte growth factor activator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,0805
Polymers77,4934
Non-polymers5871
Water3,585199
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.820, 48.230, 97.050
Angle α, β, γ (deg.)98.39, 96.24, 100.77
Int Tables number1
Space group name H-MP1

-
Components

-
Hepatocyte growth factor ... , 2 types, 2 molecules AB

#3: Protein Hepatocyte growth factor activator


Mass: 26940.518 Da / Num. of mol.: 1 / Fragment: short form HGFA
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HGFAC / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q04756, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#4: Protein/peptide Hepatocyte growth factor activator


Mass: 3962.654 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HGFAC / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q04756

-
Antibody , 2 types, 2 molecules LH

#1: Antibody antibody light chain


Mass: 23287.793 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens, Synthetic construct
Description: The protein was made using a synthetically diversified gene library and selected for tight binding to a specific target on a plastic surface. The gene library used cloned human genes as its basis
Production host: Escherichia coli (E. coli)
#2: Antibody antibody heavy chain, Fab portion only


Mass: 23302.043 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens, Synthetic construct
Description: The protein was made using a synthetically diversified gene library and selected for tight binding to a specific target on a plastic surface. The gene library used cloned human genes as its basis
Production host: Escherichia coli (E. coli)

-
Sugars / Non-polymers , 2 types, 200 molecules

#5: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 199 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45.49 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 7.5
Details: 1:1 mixture of protein complex solution at 15 mg/mL and reservoir containing 20% PEG 10000, 0.1M Hepes, pH 7.5, VAPOR DIFFUSION, SITTING DROP

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
RadiationMonochromator: Silicon 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 32514 / Num. obs: 32514 / % possible obs: 94.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -2 / Redundancy: 1.9 % / Biso Wilson estimate: 34 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 3
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.212 / Mean I/σ(I) obs: 3 / Num. unique all: 2563 / % possible all: 74.5

-
Processing

Software
NameVersionClassification
REFMAC5.1.07refinement
Blu-IceIcedata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb 1YC0, pdb 1FVD

1yc0

1fvd


Resolution: 2.2→47.51 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.917 / SU B: 6.834 / SU ML: 0.171 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -2 / ESU R: 0.33 / ESU R Free: 0.233 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24797 1535 4.7 %RANDOM
Rwork0.19278 ---
all0.195 32514 --
obs0.19537 30979 94.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.28 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å2-0.01 Å2-0.1 Å2
2---0.62 Å2-0.44 Å2
3---0.28 Å2
Refinement stepCycle: LAST / Resolution: 2.2→47.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5179 0 39 199 5417
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0215376
X-RAY DIFFRACTIONr_angle_refined_deg1.1641.9517331
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.885681
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.92723.732209
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.98415813
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9751523
X-RAY DIFFRACTIONr_chiral_restr0.0780.2817
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024054
X-RAY DIFFRACTIONr_nbd_refined0.2040.22114
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1280.2300
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2220.250
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.140.28
X-RAY DIFFRACTIONr_mcbond_it2.3692.53396
X-RAY DIFFRACTIONr_mcangle_it3.69755481
X-RAY DIFFRACTIONr_scbond_it2.8642.51980
X-RAY DIFFRACTIONr_scangle_it4.21751850
LS refinement shellResolution: 2.2→2.319 Å / Total num. of bins used: 10 /
RfactorNum. reflection
Rfree0.286 180
Rwork0.222 3758
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)
11.0868-0.21351.01181.37730.33122.95120.11940.0616-0.0512-0.16730.0071-0.01860.3380.0082-0.12640.34170.0615-0.05760.1953-0.04350.1904-19.499-23.64126.992
21.47871.1757-0.70323.0906-1.73912.98980.04580.17290.07180.2190.08520.0079-0.3661-0.1565-0.13110.50810.257-0.07310.1856-0.04240.0394-15.605-1.613-2.41
31.11630.10630.45771.3366-0.23122.2727-0.0650.04420.01730.0350.0607-0.0575-0.08510.04530.00430.27220.0707-0.03490.2278-0.05270.2085-10.542-6.30738.647
43.98991.41212.80315.04610.58143.32650.06560.05780.4111-0.8859-0.29280.551-0.37590.01460.22720.47570.2264-0.08310.1565-0.09380.1439-19.9297.1159.972
50.8729-0.31810.10791.80720.0771.4585-0.0631-0.0755-0.02270.09890.0377-0.0005-0.0077-0.02650.02540.27440.138-0.04880.2377-0.03410.1518-9.868-26.58663.279
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1LA1 - 1101 - 110
2X-RAY DIFFRACTION2LA111 - 214111 - 214
3X-RAY DIFFRACTION3HB1 - 1101 - 114
4X-RAY DIFFRACTION4HB111 - 216115 - 220
5X-RAY DIFFRACTION5AC16 - 2431 - 239

+
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