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- PDB-4bq6: Crystal structure of the RGMB-NEO1 complex form 1 -

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Basic information

Entry
Database: PDB / ID: 4bq6
TitleCrystal structure of the RGMB-NEO1 complex form 1
Components
  • (RGM DOMAIN FAMILY MEMBER B) x 2
  • NEOGENIN
KeywordsCELL ADHESION
Function / homology
Function and homology information


trans-synaptic signaling, modulating synaptic transmission / negative regulation of axon regeneration / Netrin-1 signaling / co-receptor binding / BMP receptor binding / regulation of axon regeneration / plasma membrane protein complex / positive regulation of BMP signaling pathway / myoblast fusion / intracellular vesicle ...trans-synaptic signaling, modulating synaptic transmission / negative regulation of axon regeneration / Netrin-1 signaling / co-receptor binding / BMP receptor binding / regulation of axon regeneration / plasma membrane protein complex / positive regulation of BMP signaling pathway / myoblast fusion / intracellular vesicle / endoplasmic reticulum-Golgi intermediate compartment / protein secretion / negative regulation of protein secretion / BMP signaling pathway / axonal growth cone / coreceptor activity / side of membrane / axon guidance / neuron migration / postsynaptic density membrane / cell-cell adhesion / multicellular organismal-level iron ion homeostasis / signaling receptor activity / growth cone / intracellular iron ion homeostasis / cell adhesion / cadherin binding / membrane raft / neuronal cell body / glutamatergic synapse / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / Golgi apparatus / cell surface / signal transduction / nucleoplasm / identical protein binding / membrane / plasma membrane
Similarity search - Function
Repulsive guidance molecule, C-terminal / Repulsive guidance molecule, N-terminal / Repulsive guidance molecule / Repulsive guidance molecule (RGM) C-terminus / Repulsive guidance molecule (RGM) N-terminus / Mog1/PsbP, alpha/beta/alpha sandwich / Protein Transport Mog1p; Chain A / Neogenin, C-terminal / Neogenin C-terminus / Immunoglobulin domain ...Repulsive guidance molecule, C-terminal / Repulsive guidance molecule, N-terminal / Repulsive guidance molecule / Repulsive guidance molecule (RGM) C-terminus / Repulsive guidance molecule (RGM) N-terminus / Mog1/PsbP, alpha/beta/alpha sandwich / Protein Transport Mog1p; Chain A / Neogenin, C-terminal / Neogenin C-terminus / Immunoglobulin domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Fibronectin type III domain / Fibronectin type 3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Neogenin / Repulsive guidance molecule B
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
HOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsBell, C.H. / Healey, E. / van Erp, S. / Bishop, B. / Tang, C. / Gilbert, R.J.C. / Aricescu, A.R. / Pasterkamp, R.J. / Siebold, C.
CitationJournal: Science / Year: 2013
Title: Structure of the Repulsive Guidance Molecule (Rgm)-Neogenin Signaling Hub
Authors: Bell, C.H. / Healey, E. / Van Erp, S. / Bishop, B. / Tang, C. / Gilbert, R.J.C. / Aricescu, A.R. / Pasterkamp, R.J. / Siebold, C.
History
DepositionMay 30, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 12, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: Database references
Revision 1.2Jul 17, 2013Group: Database references
Revision 1.3Apr 3, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Source and taxonomy
Category: entity_src_gen / pdbx_database_proc ...entity_src_gen / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _entity_src_gen.pdbx_host_org_cell_line / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NEOGENIN
B: NEOGENIN
C: RGM DOMAIN FAMILY MEMBER B
D: RGM DOMAIN FAMILY MEMBER B
E: RGM DOMAIN FAMILY MEMBER B
F: RGM DOMAIN FAMILY MEMBER B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,4148
Polymers140,9726
Non-polymers4422
Water5,927329
1
B: NEOGENIN
E: RGM DOMAIN FAMILY MEMBER B
F: RGM DOMAIN FAMILY MEMBER B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,7074
Polymers70,4863
Non-polymers2211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4780 Å2
ΔGint-20.6 kcal/mol
Surface area17860 Å2
MethodPISA
2
A: NEOGENIN
C: RGM DOMAIN FAMILY MEMBER B
D: RGM DOMAIN FAMILY MEMBER B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,7074
Polymers70,4863
Non-polymers2211
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4750 Å2
ΔGint-20.5 kcal/mol
Surface area17790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.320, 100.390, 103.690
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.9996, 0.01127, -0.0247), (-0.0115, -0.9999, 0.01175), (-0.02456, 0.01203, 0.9996)-23.36, -50.33, -0.1277
2given(-0.9996, -0.003685, -0.02911), (0.003562, -1, 0.004287), (-0.02912, 0.004182, 0.9996)-23.74, -50.6, -0.3116

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Components

#1: Protein NEOGENIN


Mass: 29221.842 Da / Num. of mol.: 2 / Fragment: FN-TYPE III DOMAINS 5 AND 6, RESIDUES 883-1133
Source method: isolated from a genetically manipulated source
Details: N-LINKED GLYCOSYLATION AT N940 / Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PHLSEC / Cell line (production host): HEK293T / Production host: HOMO SAPIENS (human) / References: UniProt: P97798
#2: Protein RGM DOMAIN FAMILY MEMBER B / REPULSIVE GUIDANCE MOLECULE B / DRG11-RESPONSIVE AXONAL GUIDANCE AND OUTGROWTH OF NEURITE / DRAGON


Mass: 13318.698 Da / Num. of mol.: 2 / Fragment: ECTODOMAIN, RESIDUES 50-168
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PHLSEC / Cell line (production host): HEK293T / Production host: HOMO SAPIENS (human) / References: UniProt: Q6NW40
#3: Protein RGM DOMAIN FAMILY MEMBER B / REPULSIVE GUIDANCE MOLECULE B / DRG11-RESPONSIVE AXONAL GUIDANCE AND OUTGROWTH OF NEURITE / DRAGON


Mass: 27945.352 Da / Num. of mol.: 2 / Fragment: ECTODOMAIN, RESIDUES 169-410
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PHLSEC / Cell line (production host): HEK293T / Production host: HOMO SAPIENS (human) / References: UniProt: Q6NW40
#4: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 329 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsN-ACETYL-D-GLUCOSAMINE (NAG): N-LINKED GLYCOSYLATION OF NEO1 ASN940
Sequence detailsNEO1 RESIDUES R967 AND R968 WERE BUILT AS ALANINES.

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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 % sol: 55 % / Description: NONE
Crystal growpH: 8.5
Details: 0.1 M TRIS-HCL, PH 8.5 0.2 M SODIUM ACETATE 30% PEG4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.3→57 Å / Num. obs: 42796 / % possible obs: 99.3 % / Observed criterion σ(I): 0 / Redundancy: 6 % / Biso Wilson estimate: 52.99 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 10.2
Reflection shellResolution: 2.3→2.36 Å / Redundancy: 4 % / Rmerge(I) obs: 0.84 / Mean I/σ(I) obs: 1.3 / % possible all: 95.6

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Processing

Software
NameVersionClassification
BUSTER2.11.2refinement
xia2data reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→30 Å / Cor.coef. Fo:Fc: 0.9397 / Cor.coef. Fo:Fc free: 0.9115 / SU R Cruickshank DPI: 0.29 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.301 / SU Rfree Blow DPI: 0.233 / SU Rfree Cruickshank DPI: 0.232
Details: THERE IS A AUTOCATALYTIC CLEAVAGE SITE PRESENT IN RGMB (CHAINS C/D AND D/E), WHICH IS LOCATED BETWEEN RESIDUES ASP168 AND PRO169. IN ADDITION, NEO1 RESIDUES R967 AND R968 IN (CHAIN A AND B) ...Details: THERE IS A AUTOCATALYTIC CLEAVAGE SITE PRESENT IN RGMB (CHAINS C/D AND D/E), WHICH IS LOCATED BETWEEN RESIDUES ASP168 AND PRO169. IN ADDITION, NEO1 RESIDUES R967 AND R968 IN (CHAIN A AND B) WERE BUILT AS ALANINES.
RfactorNum. reflection% reflectionSelection details
Rfree0.2665 2169 5.07 %RANDOM
Rwork0.2177 ---
obs0.2201 42757 99.42 %-
Displacement parametersBiso mean: 52.27 Å2
Baniso -1Baniso -2Baniso -3
1--0.9148 Å20 Å20 Å2
2--1.8536 Å20 Å2
3----0.9388 Å2
Refine analyzeLuzzati coordinate error obs: 0.328 Å
Refinement stepCycle: LAST / Resolution: 2.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5775 0 28 329 6132
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.015952HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.228111HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1981SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes132HARMONIC2
X-RAY DIFFRACTIONt_gen_planes852HARMONIC5
X-RAY DIFFRACTIONt_it5952HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion4.04
X-RAY DIFFRACTIONt_other_torsion18.4
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion818SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact6616SEMIHARMONIC4
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2319 175 5.78 %
Rwork0.2107 2852 -
all0.2119 3027 -
obs--99.42 %
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)
13.1165-0.3302-1.73610.69180.3053.27760.05950.7779-0.1974-0.2324-0.0093-0.26410.4614-0.0418-0.0502-0.02210.04330.05730.0497-0.1328-0.1864-0.4328-42.9682-50.7909
21.5710.0079-0.51791.0702-0.17280.85960.055-0.21610.07520.09990.1098-0.00040.1152-0.0726-0.1648-0.06960.01560.0269-0.00480.0133-0.0769-19.1607-34.8958-11.7125
33.7429-0.25912.16190.3011-0.40512.51840.01440.80910.2718-0.3110.04670.2224-0.15320.1143-0.0611-0.0039-0.0043-0.11280.02320.16-0.1447-21.7095-7.7379-51.0713
41.5338-0.1130.45731.6466-0.41581.27170.0813-0.27730.0990.1310.01740.0185-0.10020.0033-0.0987-0.09650.0121-0.0188-0.0165-0.056-0.0861-4.1358-15.4942-11.5387
52.7792-0.4418-0.09683.10570.48391.9094-0.10070.2051-0.2975-0.26060.1410.65510.2629-0.3442-0.0403-0.1907-0.0656-0.0727-0.07490.0686-0.0634-30.0853-33.4692-31.16
61.28130.02860.04742.8016-0.63561.3223-0.07990.1120.0677-0.23790.0432-0.4814-0.07330.15960.0367-0.1211-0.01960.0493-0.0784-0.0472-0.02917.3845-17.1357-30.7609
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|884 - A|984 }
2X-RAY DIFFRACTION2{ A|985 - A|1088 }
3X-RAY DIFFRACTION3{ B|884 - B|984 }
4X-RAY DIFFRACTION4{ B|985 - B|1088 }
5X-RAY DIFFRACTION5{ C|138 - D|321 }
6X-RAY DIFFRACTION6{ E|138 - F|321 }

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